From 3aeddf62d67fdde397bbf17abe77421c7c3b17e3 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Thu, 7 May 2026 10:30:05 +0200 Subject: [PATCH 1/3] Update WG Onto pages --- docs/meta/wg_onto/index.md | 3 - .../meta/wg_onto/used-ontologies/berd-nfdi.md | 42 +- .../used-ontologies/common-tlo-concepts.md | 20 - .../wg_onto/used-ontologies/daphne4nfdi.md | 40 + .../meta/wg_onto/used-ontologies/dataplant.md | 125 +- docs/meta/wg_onto/used-ontologies/fairagro.md | 86 +- docs/meta/wg_onto/used-ontologies/fairmat.md | 46 + docs/meta/wg_onto/used-ontologies/ghga.md | 48 +- docs/meta/wg_onto/used-ontologies/index.md | 97 +- .../wg_onto/used-ontologies/konsortswd.md | 105 +- docs/meta/wg_onto/used-ontologies/mardi.md | 54 +- docs/meta/wg_onto/used-ontologies/ndfi4cat.md | 74 + .../wg_onto/used-ontologies/nfdi-matwerk.md | 54 +- .../used-ontologies/nfdi4biodiversity.md | 128 +- .../wg_onto/used-ontologies/nfdi4bioimage.md | 70 +- docs/meta/wg_onto/used-ontologies/nfdi4cat.md | 28 - .../meta/wg_onto/used-ontologies/nfdi4chem.md | 142 +- .../wg_onto/used-ontologies/nfdi4culture.md | 102 +- .../used-ontologies/nfdi4datascience.md | 41 +- .../wg_onto/used-ontologies/nfdi4earth.md | 93 +- .../wg_onto/used-ontologies/nfdi4energy.md | 52 +- .../wg_onto/used-ontologies/nfdi4health.md | 149 +- .../wg_onto/used-ontologies/nfdi4immuno.md | 25 +- docs/meta/wg_onto/used-ontologies/nfdi4ing.md | 192 ++- .../wg_onto/used-ontologies/nfdi4memory.md | 83 +- .../used-ontologies/nfdi4microbiota.md | 26 +- .../wg_onto/used-ontologies/nfdi4objects.md | 108 +- docs/meta/wg_onto/used-ontologies/nfdixcs.md | 24 +- .../wg_onto/used-ontologies/punch4nfdi.md | 26 + .../meta/wg_onto/used-ontologies/text-plus.md | 75 +- justfile | 7 + package-lock.json | 1329 +++++++++++++++-- package.json | 4 +- scripts/update_collections.py | 212 +++ 34 files changed, 3005 insertions(+), 705 deletions(-) delete mode 100644 docs/meta/wg_onto/used-ontologies/common-tlo-concepts.md create mode 100644 docs/meta/wg_onto/used-ontologies/daphne4nfdi.md create mode 100644 docs/meta/wg_onto/used-ontologies/fairmat.md create mode 100644 docs/meta/wg_onto/used-ontologies/ndfi4cat.md delete mode 100644 docs/meta/wg_onto/used-ontologies/nfdi4cat.md create mode 100644 docs/meta/wg_onto/used-ontologies/punch4nfdi.md create mode 100644 justfile create mode 100644 scripts/update_collections.py diff --git a/docs/meta/wg_onto/index.md b/docs/meta/wg_onto/index.md index a33ae8f..1cb9a4e 100644 --- a/docs/meta/wg_onto/index.md +++ b/docs/meta/wg_onto/index.md @@ -39,6 +39,3 @@ The working group coordinates this work, which is essential for linking research Browse per-consortium ontology usage tables extracted from the consolidated spreadsheet. - View index: [Used Ontologies](/docs/meta/wg_onto/used-ontologies) - -Collections of ontologies, terminologies, and related resources are being ported to -the [Semantic Farm](https://semantic.farm/collection/?ror=05qj6w324) in Q2/3 in 2026. diff --git a/docs/meta/wg_onto/used-ontologies/berd-nfdi.md b/docs/meta/wg_onto/used-ontologies/berd-nfdi.md index 22815eb..20ebe1b 100644 --- a/docs/meta/wg_onto/used-ontologies/berd-nfdi.md +++ b/docs/meta/wg_onto/used-ontologies/berd-nfdi.md @@ -2,9 +2,41 @@ title: BERD@NFDI --- -Source: `/files/meta/Used_Ontologies_at_NFDI.xlsx` (sheet: BERD@NFDI) +A placeholder collection of ontologies, controlled vocabularies, and schemas +relevant for the BERD@NFDI Consortium created by the +[NFDI Section Metadata WG Ontology Harmonization and Mapping](https://github.com/nfdi-de/section-metadata-wg-onto/). +The working group is in the process of identifying BERD@NFDI Consortium members +appropriate for maintaining this collection. -|BARTOC URI|Ontology ID|Domain|License|Modularity|Format|developed / reused / only indexed / only evaluated|Used in|Comments| -|---|---|---|---|---|---|---|---|---| -|http://bartoc.org/en/node/313|STW|Economics|CC BY 4.0|maps_to: "GND, WIKIDATA, DBPEDIA, EuroVoc, TheSoz, AGROVOC, WKD, JEL, SDMX" , in RDF/XML and RDF/Turtle + RDFa for web page|skos|reused|ZBW - Leibniz Information Centre for Economics : portal for economics EconBiz|vocabulary on any economic subject| -|http://bartoc.org/en/node/485|JEL|Economics|CC BY 3.0|maps_to: "STW"|skos|reused|ZBW - Leibniz Information Centre for Economics : portal for economics EconBiz. ZBW in cooperation with KU Leuven has published translations of the original (English) version as Linked Open Data at http://zbw.eu/beta/external_identifiers/jel|The Journal of Economic Literature Classification Scheme (JEL) was created and is maintained by the American Economic Association. The AEA provides this widely used resource freely for scholarly purposes.| +## Maintainers + +- [Fidan Limani](https://semantic.farm/orcid:0000-0002-5835-2784) +- [Atif Latif](https://semantic.farm/orcid:0000-0003-3085-3031) + +Suggest a new addition to this collection +[here](https://github.com/biopragmatics/bioregistry/issues/new?template=add-collection-prefix.yml&collection=0000028&title=Add%20prefix%20X%20to%20collection%200000028). + +## Ontologies + +The following table comes from Semantic Farm collection +[`0000028`](https://semantic.farm/collection/0000028). + +| Prefix | Name | License | +| ------------------------------------------ | -------------------------------------------------------- | --------- | +| [`dfg.fo`](https://semantic.farm/dfg.fo) | DFG Classification of Subject Areas Ontology - 2020-2024 | CC-BY-4.0 | +| [`jel`](https://semantic.farm/jel) | Journal of Economic Literature Classification System | | +| [`zbw.stw`](https://semantic.farm/zbw.stw) | Standard-Thesaurus Wirtschaft | | + +## Colophon + +This page was automatically generated on 2026-05-07 using Semantic Farm +([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +by running the following commands: + +```console +$ git clone https://github.com/nfdi-de/nfdi-sections +$ cd nfdi-sections +$ uv run scripts/update_collections.py +$ git commit -am "Update WG Onto collections" +$ git push +``` diff --git a/docs/meta/wg_onto/used-ontologies/common-tlo-concepts.md b/docs/meta/wg_onto/used-ontologies/common-tlo-concepts.md deleted file mode 100644 index 13c091c..0000000 --- a/docs/meta/wg_onto/used-ontologies/common-tlo-concepts.md +++ /dev/null @@ -1,20 +0,0 @@ ---- -title: common TLO concepts ---- - -Source: `/files/meta/Used_Ontologies_at_NFDI.xlsx` (sheet: common TLO concepts) - -|Concept (NFDI pragmatic label)|BFO/OBO (CAVE: there is a difference between version 2.0 & 2020 wrt object properties!)|SIO|DOLCE (DUL)|CIDOC-CRM|PIMS-II|EMMO|W3C framework (PROV, SOSA, FOAF, etc)| -|---|---|---|---|---|---|---|---| -|location|see space|see space||?|||| -|event/occurent/process/activity|occurrent and its subclasses: process & process boundary|process - A process is an entity that is identifiable only through the unfolding of time, has temporal parts, and unless otherwise specified/predicted, cannot be identified from any instant of time in which it exists.|Event, with subclasses: Process & Action|E5 Event and 26 subclasses|||| -|method|not top level enough for BFO; If understood as special kind of process use obi:planned process or if understood as the "plan/instructions" of a process --> iao:plan specification|if understood as a special kind of process: procedure; if understood as the "plan" behind a procedure --> action specification||E7 Activity and subclasses|||| -|tool|not top level enough; but obi:device might be an option, if tool here means a physical tool (material entity) used in a scientific investigation.|not defined as such, but can be defined under specialized material entity when understood as a material entity with a destinct capability||via P188 requires production tool|||| -|material|material entity - A material entity is an independent continuant that has some portion of matter as proper or improper continuant part.|material entity - a physical entity that is spatially extended, exists as a whole at any point in time and has mass|Object from DOLCE could represent a weakly relation with "material entity" - Any physical, social, or mental object, or a substance. Following DOLCE Full, objects are always participating in some event (at least their own life), and are spatially located.|E18 Physical Thing and subclasses|||| -|time|temporal region - parent class of temporal instant and temporal interval|time is represented as information content entites (mathmatical ones more concretely) in terms of defining a time interval and time instant|Time interval - Any Region in a dimensional space that aims at representing time.|E2 Temporal Entity and subclasses|||| -|space|eigther site or one of the children of spatial region|subclasses of spatial region - A spatial region is an object contained in some region of space.||E53 Place, E92 Spacetime Volume, E94 Space Primitive or E95 Spacetime Primitive|||| -|context|there is no such thing as a context in BFO; If one wants to say that a class has to be understood in a certain way according to some discursive context, one would probably have to encode it in BFO terms as having a certain bfo:role or bfo:disposition which get's reralized in some kind of bfo:process|similar to BFO SIO has no explicit concept class, but one would use a class from its attribute branch to narrow the context of an entity|Situation - A view, consistent with ('satisfying') a Description, on a set of entities. It can also be seen as a 'relational context' created by an observer on the basis of a 'frame' (i.e. a Description).|Maybe via E7 Activity?|||| -|information|not top level enough; but there is iao:information content entity to represent information indempendenly from the material entity it is encoded/embedded in|information content entity - an object that requires some background knowledge or procedure to correctly interpret.||E73 Information Object subsumes all kinds of immaterial objects such as documents, plans, inscriptions...|||| -|quality/attributes/characteristic|specifically dependent continuant - b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. With its subclasses: quality - a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized & realizable entity - To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type.|attribute - a characteristic of some entity; with the subclasses: quality - an attribute that is intrinsically associated with its bearer (or its parts), but whose presence/absence and observed/measured value may vary, realizable entity - an attribute that is exhibited under some condition and is realized in some process|Social attribute - Any Region in a dimensional space that is used to represent some characteristic of a SocialObject, e.g. judgment values, social scalars, statistical attributes over a collection of entities, etc. Physical attribute - Physical value of a physical object, e.g. density, color, etc. Both are subclasses of Region|Maybe E13 Attribute Assignment?|||| -|variables / parameters / quantities / units||||Maybe E95 Primitive Value?|||| -|We'll need to search for existing mappings/alignments between the above listed TLOs/Terms in the next step.|||||||| diff --git a/docs/meta/wg_onto/used-ontologies/daphne4nfdi.md b/docs/meta/wg_onto/used-ontologies/daphne4nfdi.md new file mode 100644 index 0000000..61e9c37 --- /dev/null +++ b/docs/meta/wg_onto/used-ontologies/daphne4nfdi.md @@ -0,0 +1,40 @@ +--- +title: DAPHNE4NFDI +--- + +A placeholder collection of ontologies, controlled vocabularies, and schemas +relevant for the DAPHNE4NFDI Consortium created by the +[NFDI Section Metadata WG Ontology Harmonization and Mapping](https://github.com/nfdi-de/section-metadata-wg-onto/). +The working group is in the process of identifying DAPHNE4NFDI Consortium +members appropriate for maintaining this collection. + +## Maintainers + +- [Heike Görzig](https://semantic.farm/orcid:0000-0001-9121-8643) +- [Rolf Krahl](https://semantic.farm/orcid:0000-0002-1266-3819) + +Suggest a new addition to this collection +[here](https://github.com/biopragmatics/bioregistry/issues/new?template=add-collection-prefix.yml&collection=0000026&title=Add%20prefix%20X%20to%20collection%200000026). + +## Ontologies + +The following table comes from Semantic Farm collection +[`0000026`](https://semantic.farm/collection/0000026). + +| Prefix | Name | License | +| ---------------------------------- | ---------------------------- | --------- | +| [`emg`](https://semantic.farm/emg) | Electron Microscopy Glossary | CC-BY-4.0 | + +## Colophon + +This page was automatically generated on 2026-05-07 using Semantic Farm +([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +by running the following commands: + +```console +$ git clone https://github.com/nfdi-de/nfdi-sections +$ cd nfdi-sections +$ uv run scripts/update_collections.py +$ git commit -am "Update WG Onto collections" +$ git push +``` diff --git a/docs/meta/wg_onto/used-ontologies/dataplant.md b/docs/meta/wg_onto/used-ontologies/dataplant.md index ae3a613..0536ec5 100644 --- a/docs/meta/wg_onto/used-ontologies/dataplant.md +++ b/docs/meta/wg_onto/used-ontologies/dataplant.md @@ -2,51 +2,80 @@ title: DataPLANT --- -The review [Ontologies for increasing the FAIRness of plant research data](https://doi.org/10.3389/fpls.2023.1279694) provides an overview and usage guidance for ontologies in plant research. - -The table below is from the WG Ontology collection spreadsheet. - -Source: `/files/meta/Used_Ontologies_at_NFDI.xlsx` (sheet: DataPLANT) - -|Ontology ID|Domain|License|Modularity|Format|developed / reused / only indexed / only evaluated|Ontology Name|Upper Level Ontology|References|Ontology Type|DataPlant Domains|Obofoundry <br/>domain|Ontology ID Bioportal|Bioportal category|Used in|OBO dependencies|Obofoundry|OLS Url|BioPortal|Some other URL|Type Sorting|TODO: Domain aufräumen| -|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---| -|AGRO|Agronomic practices, techniques, and variables used in agronomic experiments.|CC BY 4.0|BFO|owl|only evaluated|AGRonomy Ontology|BFO|Devare et al. 2016|Plant specific ontologies|Agronomic experiments|agriculture|||GARDIAN|bfo, envo, foodon, go, iao, ncbitaxon, obi, pato, peco, po, ro, to, uo, xco|https://obofoundry.org/ontology/agro.html|https://www.ebi.ac.uk/ols/ontologies/agro|https://bioportal.bioontology.org/ontologies/AGRO||1.0| -|FLOPO|Traits and phenotypes of flowering plants|CC0 1.0|None (?!), but rich mapping to other ontologies|owl|only evaluated|Flora Phenotype Ontology|None (?!), but rich mapping to other ontologies|Hoehndorf et al. 2016|Plant specific ontologies|Flora Ontology|phenotype||Phenotype, Plant|||https://obofoundry.org/ontology/flopo.html|https://www.ebi.ac.uk/ols/ontologies/flopo|https://bioportal.bioontology.org/ontologies/FLOPO||1.0| -|PECO|Plant experimental conditions|CC BY 4.0|OBO-based|owl|reused|Plant Experimental Conditions Ontology|BFO|Cooper et al. 2018|Plant specific ontologies|Plant biology experiments.|investigations||Experimental Conditions, Phenotype, Plant|||https://obofoundry.org/ontology/peco.html|https://www.ebi.ac.uk/ols/ontologies/peco|https://bioportal.bioontology.org/ontologies/PECO||1.0| -|PO|Plant anatomy, morphology and growth and development|CC BY 4.0|OBO-based, BFO_aligned|owl|reused|Plant Ontology|BFO|Walls et al. 2012;Walls et al. 2019;Cooper et al. 2013|Plant specific ontologies|Plant anatomy and development|anatomy and development||Plant Anatomy, Plant, Plant Development|||https://obofoundry.org/ontology/po.html|http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=PO|https://bioportal.bioontology.org/ontologies/PO||1.0| -|PPEO|Plant Phenotypes and Traits (implementation of the Minimal Information About Plant Phenotyping Experiment)|CC BY 4.0||owl|only evaluated|Plant Phenotype Experiment Ontology /|None|Papoutsoglou et al. 2020|Plant specific ontologies|Plant Phenotyping|||NOT_ON_BIOPORTAL|||---|---|---|https://agroportal.lirmm.fr/ontologies/PPEO , https://github.com/MIAPPE/MIAPPE-ontology , https://fairsharing.org/1234|1.0|Real plant Ontologies <= Neither complete, not accurate, but first attempt at "sorting" the ontologies by use / domain| -|PPO|Phenology of individual plants and populations of plants|CC BY 3.0|BFO aligned|owl|only evaluated|Plant Phenology Ontology|BFO|Stucky et al. 2018|Plant specific ontologies|Plant Phenology Ontology|phenotype|||||https://obofoundry.org/ontology/ppo.html|https://www.ebi.ac.uk/ols/ontologies/ppo|https://bioportal.bioontology.org/ontologies/PPO||1.0|TODO: welche ist in welcher enthalten, welche sind gepflegt und wo sind Altlasten ...; Soll Part eines Reviews werden, welches gerade in der Mache ist| -|PSO|Biotic and abiotic stresses that a plant may encounter|CC BY 3.0|BFO|owl|only evaluated|Plant Stress Ontology|BFO|Cooper et al. 2018|Plant specific ontologies||agriculture|PLANTSO|Plant||ro|https://obofoundry.org/ontology/pso.html|https://www.ebi.ac.uk/ols/ontologies/pso|||1.0|| -|TO|Phenotypic traits in plants|CC BY 4.0|BFO|owl|reused|Plant Trait Ontology|BFO|Jaiswal 2011|Plant specific ontologies|Phenotypic traits in plants|phenotype|PTO|Phenotype, Plant|||https://obofoundry.org/ontology/to.html|https://www.ebi.ac.uk/ols/ontologies/to|https://bioportal.bioontology.org/ontologies/PTO||1.0| -|BAO|Biological screening assays and their results|||owl|only evaluated|BioAssay Ontology|None|Abeyruwan et al., 2014|General Scientific ontologies||||Molecule, Biological Process, Other, Subcellular, Chemical, Cell, Protein, Vocabularies, Physicochemical|||---|https://www.ebi.ac.uk/ols/ontologies/bao|https://bioportal.bioontology.org/ontologies/BAO||2.0|(General / Omics) Experimental stuff| -|BCO|Support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys|CC0 1.0|BFO, DwC, RO, CARO, DC, NCBITAXON, OIO, OBI, DCTERMS, IAO, SO, RDFS, OWL, PR, PCO, UBERON, ENVO, CHEBI, GO, CL|owl|only evaluated|Biological Collections Ontology|BFO|Walls et al. 2014|General Scientific ontologies|Biodiversity|organisms||All Organisms|||https://obofoundry.org/ontology/bco.html|https://www.ebi.ac.uk/ols/ontologies/bco|https://bioportal.bioontology.org/ontologies/BCO||2.0| -|BOF|Biodiversity, as developed by the National Institute for Amazonian Research|||owl|only evaluated|Biodiversity Ontology|None|Albuquerque 2011|General Scientific ontologies|Biodiversity|--|||||---|---|https://bioportal.bioontology.org/ontologies/BOF||2.0| -|BTO|Source of an enzyme comprising tissues, cell lines, cell types and cell cultures|CC BY 4.0|IAO, RO, OIO|owl|only evaluated|BRENDA Tissue and Enzyme Source Ontology|None|Gremse et al., 2011|General Scientific ontologies||anatomy and development|||||https://obofoundry.org/ontology/bto.html|https://www.ebi.ac.uk/ols/ontologies/bto|https://bioportal.bioontology.org/ontologies/BTO||2.0|(General) Tissue and cellular thingies| -|CHEBI|Molecular entities of biological interest|CC BY 4.0||owl|reused|Chemical Entities of Biological Interest Ontology|None|Degtyarenko et al. 2008|General Scientific ontologies|Chemistry|chemistry and biochemistry||Chemical|||https://obofoundry.org/ontology/chebi.html|https://www.ebi.ac.uk/ols/ontologies/chebi|https://bioportal.bioontology.org/ontologies/CHEBI||2.0|Molecular Biology things| -|CHMO|Methods used to collect data in chemical experiments|CC BY 4.0|BFO|owl|only evaluated|Chemical Methods Ontology|BFO|https://github.com/rsc-ontologies/rsc-cmo|General Scientific ontologies|Chemistry|health||Chemical|||https://obofoundry.org/ontology/chmo.html|https://www.ebi.ac.uk/ols/ontologies/chmo|https://bioportal.bioontology.org/ontologies/CHMO||2.0| -|CO|Breeder’s traits and variables|||owl|only evaluated|Crop Ontology||Shrestha et al., 2012; Arnaud et al., 2016; Arnaud et al., 2020|||||||||||||| -|DPBO|To fill the ontology gap||||developed|Data Plant Biology Ontology||https://github.com/nfdi4plants/nfdi4plants_ontology|||||||||||||| -|EDAM|computational biology, bioinformatics and bioimage informatics|||owl|only evaluated|EDAM bioinformatics operations, data types, formats, identifiers and topics|None|Ison et al., 2013|General Scientific ontologies|life-sciences & data management|||All Organisms, Biomedical Resources, Genomic and Proteomic, Other, Vocabularies|||---|https://www.ebi.ac.uk/ols/ontologies/edam|https://bioportal.bioontology.org/ontologies/EDAM||2.0|Bioinformatics stuff| -|EFO|Experimental variables|Apache license 2.0|ORDO, MONDO, CHEBI, GO, NCBITAXON, DC, NCIT, HP, FMA, OIO, OWL, UBERON, RO, PR, FBBT, OBI, OBA, IAO, SKOS, SO, BAO, DCTERMS, CLO, HANCESTRO, OGMS, PO, IDO, ZFA, RDFS, TO, CL, PATO, MPATH, DOID, FBDV, BFO, BTO, MA, MP, OMIT, UO, WBLS|owl|reused|Experimental Factor Ontology|BFO|Malone et al. 2010|General Scientific ontologies||||Experimental Conditions, Biological Process|||---|https://www.ebi.ac.uk/ols/ontologies/efo|https://bioportal.bioontology.org/ontologies/EFO||2.0| -|ENVO|Environmental systems, components and processes|CC0 1.0|CARO, CHEBI, RO, FOODON, GO, NCBITAXON, DC, UBERON, OIO, DCTERMS, IAO, SKOS, PCO, OBI, PO, RDFS, PATO, BFO, OWL, FAO, CL, SCHEMA|owl|reused|Environment Ontology|BFO|Buttigieg et al. 2013, 2016|General Scientific ontologies||environment||Experimental Conditions, Other, Physicochemical||chebi, foodon, go, ncbitaxon, pco, po, ro, uberon|https://obofoundry.org/ontology/envo.html|https://www.ebi.ac.uk/ols/ontologies/envo|https://bioportal.bioontology.org/ontologies/ENVO||2.0| -|GEOSPECIES|Integration of species concepts with species occurrences, gene sequences, images, references and geographical information||EO|owl|only evaluated|GeoSpecies Ontology|None|http://lod.geospecies.org/|General Scientific ontologies||||Other|||---|---|https://bioportal.bioontology.org/ontologies/GEOSPECIES||2.0| -|GO|Function of genes and gene products|CC BY 4.0|OIO, DC, IAO, DCTERMS, RDFS, RO, OWL|owl|only evaluated|Gene Ontology|None|Ashburner et al. 2000;Gene Ontology Consortium 2023|General Scientific ontologies|Biology|biological systems||Genomic and Proteomic||cl, go/extensions/go-bridge-to-nifstd.owl, ncbitaxon, ro, uberon|https://obofoundry.org/ontology/go.html|https://www.ebi.ac.uk/ols/ontologies/go|||2.0| -|MMO|Methods used to make clinical and phenotype measurements|CC0 1.0||owl|only evaluated|Measurement Method Ontology|None|Smith et al., 2013|General Scientific ontologies||health||Phenotype|||https://obofoundry.org/ontology/mmo.html|https://www.ebi.ac.uk/ols/ontologies/mmo|https://bioportal.bioontology.org/ontologies/MMO||2.0| -|MOD|Protein chemical modifications, classified by molecular structure or amino acid|CC BY 4.0||owl|reused|Protein modification (PSI-MOD)||Montecchi-Palazzi et al. 2008|General Scientific ontologies||chemistry and biochemistry|||||https://obofoundry.org/ontology/mod.html|https://www.ebi.ac.uk/ols/ontologies/mod|||2.0| -|MS|proteomics mass spectrometry|CC BY 4.0||owl|reused|PSI Mass Spectrometry Ontology|None|Mayer et al., 2013|General Scientific ontologies|Chemistry|investigations||Experimental Conditions, Protein||pato, uo|https://obofoundry.org/ontology/ms.html|https://www.ebi.ac.uk/ols/ontologies/ms|https://bioportal.bioontology.org/ontologies/MS||2.0| -|MSIO|mass-spectrometry and nmr-spectroscopy based metabolomics experiments and fluxomics studies||BFO|owl|only evaluated|Metabolomics Standards Initiative Ontology (MSIO)|BFO|Rocca-Serra, 2018|General Scientific ontologies||||NOT_ON_BIOPORTAL|||---|https://www.ebi.ac.uk/ols/ontologies/msio|---||2.0| -|NCBITAXON|NCBI organismal taxonomy|CC0 1.0|OIO, DCTERMS, IAO|owl|reused|National Center for Biotechnology Information (NCBI) Organismal Classification|None|Federhen 2012|General Scientific ontologies|Taxonomy|organisms||Taxonomic Classification|||https://obofoundry.org/ontology/ncbitaxon.html|https://www.ebi.ac.uk/ols/ontologies/ncbitaxon|https://bioportal.bioontology.org/ontologies/NCBITAXON||2.0|(General) Taxonomy stuff Missing: full-blown Leipzig catalogue of vascular plants| -|NCIT|Broad coverage of the cancer domain|CC BY 4.0||owl|reused|National Cancer Institute Thesaurus|None ??|https://ncit.nci.nih.gov|General Scientific ontologies||health|||||https://obofoundry.org/ontology/ncit.html|https://www.ebi.ac.uk/ols/ontologies/ncit|https://bioportal.bioontology.org/ontologies/NCIT||2.0| -|OBI|Life-science and clinical investigations|CC BY 4.0|BFO|owl|reused|Ontology for Biomedical Investigations|BFO|Brinkman et al. 2010;<br/>Bandrowski et al. 2016|General Scientific ontologies|Biomedicine|investigations||Experimental Conditions|||https://obofoundry.org/ontology/obi.html|https://www.ebi.ac.uk/ols/ontologies/obi|https://bioportal.bioontology.org/ontologies/OBI||2.0|(General) Experimental setup, descriptions| -|OMP|phenotypes observed in all microbes|CC BY 3.0|imports terms from PATO, CHEBI, GO|owl|reused|Ontology of Microbial Phenotypes|||General Scientific ontologies|microbiology|||Phenotype|||||https://bioportal.bioontology.org/ontologies/OMP|||| -|PATO|Phenotypic qualities (properties, attributes or characteristics)|CC BY 3.0|BFO|owl|reused|Phenotype And Trait Ontology|BFO|Gkoutos et al. 2018|General Scientific ontologies|Phenotypic Quality Ontology|phenotype||Phenotype|||https://obofoundry.org/ontology/pato.html|https://www.ebi.ac.uk/ols/ontologies/pato|https://bioportal.bioontology.org/ontologies/PATO||2.0|| -|PCO|Material entities, qualities, and processes related to collections of interacting organisms such as populations and communities|CC0 1.0|BFO|owl|only evaluated|Population and Community Ontology|BFO|Walls et al. 2014|General Scientific ontologies||environment||All Organisms, Other||bfo, caro, envo, go, iao, ncbitaxon, pato, ro|https://obofoundry.org/ontology/pco.html|https://www.ebi.ac.uk/ols/ontologies/pco|https://bioportal.bioontology.org/ontologies/PCO||2.0| -|STATO|statistical tests, conditions of application, and information needed or resulting from statistical methods||BFO|owl|only evaluated|Statistics Ontology|BFO|https://github.com/ISA-tools/stato|General Scientific ontologies||information technology||Biomedical Resources, Experimental Conditions|||https://obofoundry.org/ontology/stato.html|https://www.ebi.ac.uk/ols/ontologies/stato|https://bioportal.bioontology.org/ontologies/STATO||2.0| -|SWO|software tools, their types, tasks, versions, provenance and associated data|CC BY 4.0|BFO, RO, OBI|owl|only evaluated|Software Ontology|BFO|Malone et al., 2014|General Scientific ontologies|life-sciences & data management|information technology||Experimental Conditions, Biomedical Resources|||https://obofoundry.org/ontology/swo.html|https://www.ebi.ac.uk/ols/ontologies/swo|||2.0| -|UO|Metrical units for use in conjunction with PATO|CC BY 3.0||owl|reused|Unit Ontology|None|Gkoutos et al. 2012|General Scientific ontologies|Scientific units|phenotype||Phenotype|||https://obofoundry.org/ontology/uo.html|https://www.ebi.ac.uk/ols/ontologies/uo|https://bioportal.bioontology.org/ontologies/UO||2.0| -|BFO|Standardizes upper level structure of OBO ontologies|CC BY 4.0||owl|only evaluated|Basic Formal Ontology||Arp et al. 2015|Upper level ontologies||upper||Upper Level Ontology|||https://obofoundry.org/ontology/ro.html||https://bioportal.bioontology.org/ontologies/BFO||3.0| -|RO|Standardizes relations in obo foundry ontologies|CC0 1.0||owl|reused|Relations Ontology||https://oborel.github.io/obo-relations/|Upper level ontologies||upper|||||https://obofoundry.org/ontology/ro.html|https://www.ebi.ac.uk/ols/ontologies/ro|||3.0| -|EO||CC BY 4.0|||only evaluated|Plant Environment Ontology, This ontology is deprecated! Consider using: peco|||XXX Deprecated|This ontology is deprecated! Consider using: peco|environment||Other|||https://obofoundry.org/ontology/eo.html||||4.0|Environmental / Biodiversity like stuff| -|GAZ||CC0 1.0||owl|only evaluated|Gazetteer. This ontology is inactive.|None ??||XXX Deprecated||environment|||||https://obofoundry.org/ontology/gaz.html|https://www.ebi.ac.uk/ols/ontologies/gaz|https://bioportal.bioontology.org/ontologies/GAZ||4.0| -|NEWT|||||only evaluated|NEWT UniProt Taxonomy||||Taxonomy|organisms||NOT_ON_BIOPORTAL|||---|---|---||4.0| -|PAE|||||only evaluated|Plant Anatomy, REPLACED BY: Plant Ontology (PO).|||XXX Deprecated|REPLACED BY: Plant Ontology (PO).|||Plant Anatomy, Plant|||---|---|https://bioportal.bioontology.org/ontologies/PAE||4.0| +A collection of ontologies, controlled vocabularies, and schemas relevant for +the DataPLANT Consortium seeded from corresponding the +[TIB OLS collection](https://service.tib.eu/terminology/collections/dataplant). +See also a [recent review](https://doi.org/10.3389/fpls.2023.1279694) on +ontologies for plant research data. + +## Maintainers + +- [Kathryn Dumschott](https://semantic.farm/orcid:0000-0002-9905-4011) +- [Angela Kranz](https://semantic.farm/orcid:0000-0002-8000-0400) +- [Hannah Dörpholz](https://semantic.farm/orcid:0000-0002-0476-9699) + +Suggest a new addition to this collection +[here](https://github.com/biopragmatics/bioregistry/issues/new?template=add-collection-prefix.yml&collection=0000023&title=Add%20prefix%20X%20to%20collection%200000023). + +## Ontologies + +The following table comes from Semantic Farm collection +[`0000023`](https://semantic.farm/collection/0000023), which is automatically +synced from the TIB Terminology Service collection +[`dataplant`](https://service.tib.eu/terminology/collections/dataplant). + +| Prefix | Name | License | +| -------------------------------------------------------------------- | ------------------------------------------ | ------------ | +| [`AGRO`](https://semantic.farm/agro) | Agronomy Ontology | CC-BY-4.0 | +| [`bao`](https://semantic.farm/bao) | BioAssay Ontology | CC-BY-SA-4.0 | +| [`BCO`](https://semantic.farm/bco) | Biological Collections Ontology | CC0-1.0 | +| [`BFO`](https://semantic.farm/bfo) | Basic Formal Ontology | CC-BY-4.0 | +| [`bioportal.bof`](https://semantic.farm/bioportal.bof) | Biodiversity Ontology | | +| [`bioportal.geospecies`](https://semantic.farm/bioportal.geospecies) | GeoSpecies Ontology | | +| [`BTO`](https://semantic.farm/bto) | BRENDA Tissue Ontology | CC-BY-4.0 | +| [`CHEBI`](https://semantic.farm/chebi) | Chemical Entities of Biological Interest | CC-BY-4.0 | +| [`CHMO`](https://semantic.farm/chmo) | Chemical Methods Ontology | CC-BY-4.0 | +| [`COB`](https://semantic.farm/cob) | Core Ontology for Biology and Biomedicine | CC0-1.0 | +| [`dpbo`](https://semantic.farm/dpbo) | DataPLANT Biology Ontology | CC-BY-4.0 | +| [`edam`](https://semantic.farm/edam) | EDAM Ontology | CC-BY-SA-4.0 | +| [`EFO`](https://semantic.farm/efo) | Experimental Factor Ontology | Apache-2.0 | +| [`ENVO`](https://semantic.farm/envo) | Environment Ontology | CC0-1.0 | +| [`EO`](https://semantic.farm/eo) | Plant Environment Ontology | CC-BY-4.0 | +| [`FLOPO`](https://semantic.farm/flopo) | Flora Phenotype Ontology | CC0-1.0 | +| [`GAZ`](https://semantic.farm/gaz) | Gazetteer | CC0-1.0 | +| [`GO`](https://semantic.farm/go) | Gene Ontology | CC-BY-4.0 | +| [`MMO`](https://semantic.farm/mmo) | Measurement method ontology | CC0-1.0 | +| [`MOD`](https://semantic.farm/mod) | Protein modification | CC-BY-4.0 | +| [`MS`](https://semantic.farm/ms) | Mass spectrometry ontology | CC-BY-3.0 | +| [`msio`](https://semantic.farm/msio) | Metabolomics Standards Initiative Ontology | CC-BY-3.0 | +| [`NCBITaxon`](https://semantic.farm/ncbitaxon) | NCBI Taxonomy | CC0-1.0 | +| [`NCIT`](https://semantic.farm/ncit) | NCI Thesaurus | CC-BY-4.0 | +| [`OBI`](https://semantic.farm/obi) | Ontology for Biomedical Investigations | CC-BY-4.0 | +| [`OMP`](https://semantic.farm/omp) | Ontology of Microbial Phenotypes | CC-BY-3.0 | +| [`PATO`](https://semantic.farm/pato) | Phenotype And Trait Ontology | CC-BY-3.0 | +| [`PCO`](https://semantic.farm/pco) | Population and Community Ontology | CC0-1.0 | +| [`PECO`](https://semantic.farm/peco) | Plant Experimental Conditions Ontology | CC-BY-4.0 | +| [`PO`](https://semantic.farm/po) | Plant Ontology | CC-BY-4.0 | +| [`ppeo`](https://semantic.farm/ppeo) | Plant Phenotype Experiment Ontology | CC-BY-4.0 | +| [`PPO`](https://semantic.farm/ppo) | Plant Phenology Ontology | CC-BY-3.0 | +| [`PSO`](https://semantic.farm/pso) | Plant Stress Ontology | CC-BY-4.0 | +| [`RO`](https://semantic.farm/ro) | Relation Ontology | CC0-1.0 | +| [`STATO`](https://semantic.farm/stato) | The Statistical Methods Ontology | CC-BY-3.0 | +| [`SWO`](https://semantic.farm/swo) | Software ontology | CC-BY-4.0 | +| [`TO`](https://semantic.farm/to) | Plant Trait Ontology | CC-BY-4.0 | +| [`UBERON`](https://semantic.farm/uberon) | Uber Anatomy Ontology | CC-BY-3.0 | +| [`UO`](https://semantic.farm/uo) | Units of measurement ontology | CC-BY-3.0 | + +## Colophon + +This page was automatically generated on 2026-05-07 using Semantic Farm +([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +by running the following commands: + +```console +$ git clone https://github.com/nfdi-de/nfdi-sections +$ cd nfdi-sections +$ uv run scripts/update_collections.py +$ git commit -am "Update WG Onto collections" +$ git push +``` diff --git a/docs/meta/wg_onto/used-ontologies/fairagro.md b/docs/meta/wg_onto/used-ontologies/fairagro.md index 0aece04..b1363be 100644 --- a/docs/meta/wg_onto/used-ontologies/fairagro.md +++ b/docs/meta/wg_onto/used-ontologies/fairagro.md @@ -2,32 +2,60 @@ title: FAIRagro --- -Source: `/files/meta/Used_Ontologies_at_NFDI.xlsx` (sheet: FAIRagro) - -|Ontology ID|Ontology name|Domain|License|Format (uncontrolled)|Format|developed / reused / only indexed / only evaluated|Modularity|Obofoundry|OLS URL|Bioportal|Github|File URL|Other URL|Description|Comments| -|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---| -|BCO|Biological Collections Ontology|biology|CC0 1.0|OWL|owl|reused|BFO & OBO based|https://ontobee.org/ontology/BCO|https://www.ebi.ac.uk/ols/ontologies/bco|https://bioportal.bioontology.org/ontologies/BCO|https://github.com/BiodiversityOntologies/bco|https://bioportal.bioontology.org/ontologies/BCO||OBO: The Biological Collections Ontology (BCO) is a being developed as an application ontology as part of the Biocode Commons project, within the OBO Foundry framework. The goal of the BCO is to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys.<br/><br/>GFBio: The biological collection ontology includes consideration of the distinctions between individuals, organisms, voucher specimens, lots, and samples the relations between these entities, and processes governing the creation and use of "samples". Within scope as well are properties including collector, location, time, storage environment, containers, institution, and collection identifiers.| -|ChEBI|Chemical Entities of Biological Interest Ontology|chemistry|CC BY 4.0|OWL|owl|reused|OBO_based|https://obofoundry.org/ontology/chebi.html|https://www.ebi.ac.uk/ols/ontologies/chebi|https://bioportal.bioontology.org/ontologies/CHEBI|https://github.com/ebi-chebi/ChEBI|https://bioportal.bioontology.org/ontologies/CHEBI|http://www.ebi.ac.uk/chebi|GitHub: Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds. The term ‘molecular entity’ refers to any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity.<br/><br/>Other source: A structured classification of chemical compounds of biological relevance.| -|ENVO|Environment Ontology|environmental|CC0 1.0|OWL|owl|reused|BFO & OBO based|https://obofoundry.org/ontology/envo.html|https://www.ebi.ac.uk/ols/ontologies/envo|https://bioportal.bioontology.org/ontologies/ENVO|https://github.com/EnvironmentOntology/envo|https://raw.githubusercontent.com/EnvironmentOntology/envo/master/envo.owl|http://environmentontology.org/|BioPortal: The most up-to-date information about ENVO is available here: http://www.obofoundry.org/ontology/envo.html EnvO is an OBO Foundry and Library ontology for the concise, controlled description of environmental entities such as ecosystems, environmental processes, and environmental qualities. It closely interoperates with a broad collection of other OBO ontologies and is used in a diverse range of projects.| -|FLOPO|Flora Phenotype Ontology|anatomical|CC BY 3.0|OWL|owl|reused||https://obofoundry.org/ontology/flopo.html|https://www.ebi.ac.uk/ols/ontologies/flopo|https://bioportal.bioontology.org/ontologies/FLOPO|https://github.com/flora-phenotype-ontology/flopoontology|https://github.com/flora-phenotype-ontology/flopoontology/tree/master/ontology||BioPortal: The Flora Phenotype Ontology is an ontology of phenotypes reported in Floras. The original version was developed at the pro-iBiosphere Hackathon in Leiden. This is the pre-classified version of the ontology; the original OWL file is at https://github.com/flora-phenotype-ontology/flopoontology/blob/master/ontology/flopo.owl The Flora Phenotype Ontology is generated from the Flora Malesiana, Flora Gabon, Flora of Central Africa, and a collection of Kew's African Floras. Every class in the ontology has at least one taxon annotation. The (draft) taxon annotation are available at http://jagannath.pdn.cam.ac.uk/plant/flora/clean-rerun/| -|NCBITAXON|National Center for Biotechnology Information Organismal Classification|biology|CC0 1.0|OWL|owl|reused|OBO_based|https://obofoundry.org/ontology/ncbitaxon.html|https://www.ebi.ac.uk/ols/ontologies/ncbitaxon|https://bioportal.bioontology.org/ontologies/NCBITAXON|https://github.com/obophenotype/ncbitaxon|https://bioportal.bioontology.org/ontologies/NCBITAXON|https://www.ncbi.nlm.nih.gov/taxonomy|OBO: The NCBITaxon ontology is an automatic translation of the NCBI taxonomy database into obo/owl.<br/><br/>NCBI: The Taxonomy Database is a curated classification and nomenclature for all of the organisms in the public sequence databases. This currently represents about 10% of the described species of life on the planet.| -|OBOE|The Extensible Observation Ontology|environmental|CC BY 3.0|OWL|owl|reused||||https://bioportal.bioontology.org/ontologies/OBOE|https://github.com/NCEAS/oboe|https://bioportal.bioontology.org/ontologies/OBOE||BioPortal: The Extensible Observation Ontology (OBOE) is a formal ontology for capturing the semantics of scientific observation and measurement. The ontology supports researchers to add detailed semantic annotations to scientific data, thereby clarifying the inherent meaning of scientific observations| -|PATO|The Phenotype And Trait Ontology|anatomical|CC BY 3.0|OWL|owl|reused|OBO_based|https://obofoundry.org/ontology/pato.html|https://www.ebi.ac.uk/ols/ontologies/pato|https://bioportal.bioontology.org/ontologies/PATO|https://github.com/pato-ontology/pato/|https://bioportal.bioontology.org/ontologies/PATO||Obo & BioPortal: Phenotypic qualities (properties). This ontology can be used in conjunction with other ontologies such as GO or anatomical ontologies to refer to phenotypes. Examples of qualities are red, ectopic, high temperature, fused, small, edematous and arrested.| -|PO|Plant Ontology|biology|CC BY 4.0|OWL|owl|reused|BFO & OBO based|https://obofoundry.org/ontology/po.html|https://www.ebi.ac.uk/ols/ontologies/po|https://bioportal.bioontology.org/ontologies/PO|https://github.com/Planteome/plant-ontology|https://bioportal.bioontology.org/ontologies/PO|https://www.plantontology.org|PO Consortium: The Plant Ontology is a controlled vocabulary (ontology) that describes plant anatomy and morphology and stages of development for all plants. The goal of the PO is to establish a semantic framework for meaningful cross-species queries across gene expression and phenotype data sets from plant genomics and genetics experiments.<br/><br/>BioPortal: The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data. The PO is under active development to expand to encompass terms and annotations from all plants.| -|PTO|Plant Trait Ontology|anatomical|CC BY 4.0|OWL|owl|reused|BFO|https://obofoundry.org/ontology/to.html|https://www.ebi.ac.uk/ols/ontologies/to|https://bioportal.bioontology.org/ontologies/PTO|https://github.com/Planteome/plant-trait-ontology|https://bioportal.bioontology.org/ontologies/PTO|PO, TO, PECO, PSO: https://browser.planteome.org/amigo|BioPortal: A controlled vocabulary to describe phenotypic traits in plants. Each trait is a distinguishable feature, characteristic, quality or phenotypic feature of a developing or mature plant, or a plant part.| -|SWEET|Semantic Web for Earth and Environment Technology Ontology|geo-sciences|CC0 1.0|OWL|owl|reused||||https://bioportal.bioontology.org/ontologies/SWEET|https://github.com/ESIPFed/sweet|https://bioportal.bioontology.org/ontologies/SWEET<br/><br/>http://sweetontology.net/sweetAll||BioPortal: The Semantic Web for Earth and Environmental Terminology is a mature foundational ontology that contains over 6000 concepts organized in 200 ontologies represented in OWL. Top level concepts include Representation (math, space, science, time, data), Realm (Ocean, Land Surface, Terrestrial Hydroshere, Atmosphere, etc.), Phenomena (macro-scale ecological and physical), Processes (micro-scale physical, biological, chemical, and mathematical), Human Activities (Decision, Commerce, Jurisdiction, Environmental, Research). Originally developed by NASA Jet Propulsion Labs under Rob Raskin, SWEET is now officially under the governance of the ESIP foundation.| -|GEONAMES|The Geonames geographical database|geo-sciences|CC BY 4.0|OWL|owl|reused||||||https://www.geonames.org/ontology/ontology_v3.3.rdf|http://www.geonames.org/|GeoNames: The GeoNames geographical database is available for download free of charge under a creative commons attribution license. It contains over 25 million geographical names and consists of over 11 million unique features whereof 4.8 million populated places and 13 million alternate names. All features are categorized into one out of nine feature classes and further subcategorized into one out of 645 feature codes... GeoNames is integrating geographical data such as names of places in various languages, elevation, population and others from various sources.<br/><br/>W3C: The GeoNames Ontology makes it possible to add geospatial semantic information to the Word Wide Web. All over 6.2 million geonames toponyms now have a unique URL with a corresponding RDF web service. Other services describe the relation between toponyms.<br/><br/>European Comission: The Geonames ontology provides elements of description for geographical features defined in the geonames.org data base| -|GAZ|Gazetteer. This ontology is inactive.|environment|CC0 1.0|OWL|owl|only indexed||https://obofoundry.org/ontology/gaz.html|https://www.ebi.ac.uk/ols/ontologies/gaz|https://bioportal.bioontology.org/ontologies/GAZ?p=summary|https://github.com/EnvironmentOntology/gaz|http://environmentontology.github.io/gaz/|https://www.ebi.ac.uk/ols/ontologies/gaz<br/><br/>http://environmentontology.github.io/gaz/|GAZ: GAZ represents places through their names using an ontological approach to promote semantic coherence. All entities in GAZ can be treated as instances of environments (see the ENVO repository).| -|DCAT|Data Catalog Vocabulary|vocabulary|W3C License|RDF|owl|reused|W3C_based|||https://bioportal.bioontology.org/ontologies/DCAT||DCAT V2: https://www.w3.org/TR/vocab-dcat/<br/><br/>DCAT V3: https://www.w3.org/TR/vocab-dcat-3/||W3C: DCAT 3 supersedes DCAT 2 [VOCAB-DCAT-2], but it does not make it obsolete. DCAT 3 maintains the DCAT namespace as its terms preserve backward compatibility with DCAT 2. DCAT 3 relaxes constraints and adds new classes and properties, but these changes do not break the definition of previous terms.<br/><br/>Any new implementation is expected to adopt DCAT 3, while the existing implementations do not need to upgrade to it, unless they want to use the new features. In particular, current DCAT 2 deployments that do not overlap with the DCAT 3 new features (e.g., versioning, dataset series and inverse properties) don't need to change anything to remain in conformance with DCAT 3.| -|SCHEMA||vocabulary|CC BY-SA 3.0|Various formats<br/>https://schema.org/docs/developers.html|rdf|reused||||||https://schema.org<br/><br/>Various formats<br/>https://schema.org/docs/developers.html|https://schema.org|schema.org: These vocabularies cover entities, relationships between entities and actions, and can easily be extended through a well-documented extension model.| -|PROV-O|The PROV Ontology|ontology|W3C License||owl|reused|W3C_based|||||Namespace: http://www.w3.org/ns/prov#<br/><br/>OWL encoding: http://www.w3.org/TR/prov-o/|https://www.w3.org/TR/prov-o/|w3c: It provides a set of classes, properties, and restrictions that can be used to represent and interchange provenance information generated in different systems and under different contexts. It can also be specialized to create new classes and properties to model provenance information for different applications and domains.| -|FOAF|Friend of a Friend|ontology, Semantic Web|CC BY 1.0|RDF, OWL|owl|reused|W3C_based|||https://bioportal.bioontology.org/ontologies/FOAF||http://xmlns.com/foaf/0.1/||| -|DCTERMS|Dublin Core terms|metadata standard|CC BY 4.0||rdf|reused||||||http://purl.org/dc/terms/<br/><br/>http://purl.org/dc/elements/1.1/|https://www.dublincore.org/specifications/dublin-core/|dublincore.org: The Dublin Core™ metadata standard is a simple yet effective element set for describing a wide range of networked resources. The Dublin Core™ standard includes two levels: Simple and Qualified. Simple Dublin Core™ comprises fifteen elements; Qualified Dublin Core™ includes three additional elements (Audience, Provenance and RightsHolder), as well as a group of element refinements (also called qualifiers) that refine the semantics of the elements in ways that may be useful in resource discovery.| -|openDS|Open Digital Specimens|data model||||reused|||||https://github.com/DiSSCo/opends|||GitHub: openDS is a specification of Digital Specimen and other related object type definitions essential to mass digitization of natural science collections and their digital use in a new generation of infrastructure and applications. For the principal digital object types corresponding to major categories of collections and specimens’ data, openDS defines the structure and content of each object type, and the operations that can act upon them.| -|ODS|The Ontology for open Digital Specimens (ODS)||||owl|reused|||||https://github.com/DiSSCo/openDS/blob/master/ods-ontology/ods-ont-intro.md|||GitHub: The Ontology for open Digital Specimens (ODS) situates open Digital Specimens in the relevant OBO Foundry ontologies and extends from those roots to define the new concepts needed to support mass digitization and Digital Specimens on the Internet.<br/><br/>| -|ABCD-EFG|Access to Biological Collection Data Extended for Geosciences.||CC BY 4.0||xsd|reused|||||||https://terms.tdwg.org/wiki/ABCD_2<br/>Currently offline<br/><br/>Schema abcdefg.xsd: https://efg.geocase.eu/sites/default/documentation/html/efg.html|ABCD Schema is a comprehensive XML-based standard for the access to and exchange of natural history collection and observational data.<br/>ABCD allows a detailed, atomized mapping of information about collection specimens and results of observations in the field. Data from any arbitrarily structured database can be mapped using freely available open source software (BioCASE provider software - www.biocase.org).| -|SKOS|Simple Knowledge Organisation System|terminologies||SKOS|skos|only indexed|W3C_based|||||http://www.w3.org/2004/02/skos/core#|https://www.w3.org/2004/02/skos/<br/><br/>https://www.w3.org/TR/skos-reference/|SKOS is an area of work developing specifications and standards to support the use of knowledge organization systems (KOS) such as thesauri, classification schemes, subject heading systems and taxonomies within the framework of the Semantic Web.| -|WLMO||||||reused||||||||| -|SSN|Semantic Sensor Network Ontology|sensors and their observations|W3C License|OWL|owl|reused|W3C_based, DUL aligned, OBOE_aligned, PROV-O_aligned, O&M_aligned|||https://bioportal.bioontology.org/ontologies/SSN||http://purl.oclc.org/NET/ssnx/ssn|https://www.w3.org/2005/Incubator/ssn/ssnx/ssn<br/><br/>https://service.tib.eu/ts4tib/ontologies/ssn|Bioportal: This ontology describes sensors, actuators and observations, and related concepts. It does not describe domain concepts, time, locations, etc. these are intended to be included from other ontologies via OWL imports.| -|SOSA|Sensor, Observation, Sample and Actuator (SOSA) Ontology|vocabulary|W3C License|OWL|owl|reused|W3C_based, DUL aligned, OBOE_aligned, PROV-O_aligned, O&M_aligned|||||http://liveschema.eu/dataset/lov_sosa||Ghislain Atemezing: This ontology is based on the SSN Ontology by the W3C Semantic Sensor Networks Incubator Group (SSN-XG), together with considerations from the W3C/OGC Spatial Data on the Web Working Group.<br/><br/>Article https://doi.org/10.1016/j.websem.2018.06.003 : SOSA is the result of rethinking the W3C-XG Semantic Sensor Network (SSN) ontology based on changes in scope and target audience, technical developments, and lessons learned over the past years. SOSA also acts as a replacement of SSN’s Stimulus Sensor Observation (SSO) core.<br/><br/>Observation, sampling and sample, time and more: https://www.youtube.com/watch?v=BHBU5gYAmV4| -|AO|Annotation Ontology|vocabulary|CC BY 3.0|OWL|owl|reused|FOAF, PAV, DCT|||||https://raw.githubusercontent.com/annotation-ontology/annotation-ontology/master/annotation.owl|https://code.google.com/archive/p/annotation-ontology/wikis/Homepage.wiki|CC BY 3.0|Ontology & Term PURLs don't resolve anymore| +A placeholder collection of ontologies, controlled vocabularies, and schemas +relevant for the FAIRagro Consortium created by the +[NFDI Section Metadata WG Ontology Harmonization and Mapping](https://github.com/nfdi-de/section-metadata-wg-onto/). +The working group is in the process of identifying FAIRagro Consortium members +appropriate for maintaining this collection. + +## Maintainers + +- [Gabriel Schneider](https://semantic.farm/orcid:0000-0001-6573-3115) + +Suggest a new addition to this collection +[here](https://github.com/biopragmatics/bioregistry/issues/new?template=add-collection-prefix.yml&collection=0000033&title=Add%20prefix%20X%20to%20collection%200000033). + +## Ontologies + +The following table comes from Semantic Farm collection +[`0000033`](https://semantic.farm/collection/0000033). + +| Prefix | Name | License | +| ---------------------------------------------- | ---------------------------------------------------------- | --------------------------------------------------------------------------------- | +| [`BCO`](https://semantic.farm/bco) | Biological Collections Ontology | CC0-1.0 | +| [`CHEBI`](https://semantic.farm/chebi) | Chemical Entities of Biological Interest | CC-BY-4.0 | +| [`dcat`](https://semantic.farm/dcat) | Data Catalog | CC-BY-4.0 | +| [`dcterms`](https://semantic.farm/dcterms) | Dublin Core Metadata Initiative Terms | | +| [`ENVO`](https://semantic.farm/envo) | Environment Ontology | CC0-1.0 | +| [`FLOPO`](https://semantic.farm/flopo) | Flora Phenotype Ontology | CC0-1.0 | +| [`foaf`](https://semantic.farm/foaf) | Friend of a Friend | CC-BY-1.0 | +| [`GAZ`](https://semantic.farm/gaz) | Gazetteer | CC0-1.0 | +| [`geonames`](https://semantic.farm/geonames) | GeoNames | CC-BY-4.0 | +| [`legacy.ao`](https://semantic.farm/legacy.ao) | Annotation Ontology | CC-BY-3.0 | +| [`NCBITaxon`](https://semantic.farm/ncbitaxon) | NCBI Taxonomy | CC0-1.0 | +| [`oboe`](https://semantic.farm/oboe) | The Extensible Observation Ontology | CC-BY-3.0 | +| [`PATO`](https://semantic.farm/pato) | Phenotype And Trait Ontology | CC-BY-3.0 | +| [`PO`](https://semantic.farm/po) | Plant Ontology | CC-BY-4.0 | +| [`prov`](https://semantic.farm/prov) | PROV Namespace | | +| [`schema`](https://semantic.farm/schema) | Schema.org | | +| [`skos`](https://semantic.farm/skos) | Simple Knowledge Organization System | | +| [`sosa`](https://semantic.farm/sosa) | Sensor, Observation, Sample, and Actuator Ontology | [Custom](http://www.w3.org/Consortium/Legal/2015/copyright-software-and-document) | +| [`ssn`](https://semantic.farm/ssn) | Semantic Sensor Network Ontology | [Custom](http://www.w3.org/Consortium/Legal/2015/copyright-software-and-document) | +| [`sweet`](https://semantic.farm/sweet) | Semantic Web for Earth and Environment Technology Ontology | CC0-1.0 | +| [`tdwg.abcd`](https://semantic.farm/tdwg.abcd) | Access to Biological Collection Data Schema | | +| [`TO`](https://semantic.farm/to) | Plant Trait Ontology | CC-BY-4.0 | +| [`wlmo`](https://semantic.farm/wlmo) | Wildlife Monitoring Ontology | CC-BY-4.0 | + +## Colophon + +This page was automatically generated on 2026-05-07 using Semantic Farm +([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +by running the following commands: + +```console +$ git clone https://github.com/nfdi-de/nfdi-sections +$ cd nfdi-sections +$ uv run scripts/update_collections.py +$ git commit -am "Update WG Onto collections" +$ git push +``` diff --git a/docs/meta/wg_onto/used-ontologies/fairmat.md b/docs/meta/wg_onto/used-ontologies/fairmat.md new file mode 100644 index 0000000..5dd2fff --- /dev/null +++ b/docs/meta/wg_onto/used-ontologies/fairmat.md @@ -0,0 +1,46 @@ +--- +title: FAIRmat +--- + +A placeholder collection of ontologies, controlled vocabularies, and schemas +relevant for the FAIRmat Consortium seeded from corresponding the +[TIB OLS collection](https://service.tib.eu/terminology/collections/fairmat). +The +[NFDI Section Metadata WG Ontology Harmonization and Mapping](https://github.com/nfdi-de/section-metadata-wg-onto/) +is in the process of identifying FAIRmat Consortium members appropriate for +maintaining this collection. + +## Maintainers + +- [Markus Kühbach](https://semantic.farm/orcid:0000-0002-7117-5196) + +Suggest a new addition to this collection +[here](https://github.com/biopragmatics/bioregistry/issues/new?template=add-collection-prefix.yml&collection=0000024&title=Add%20prefix%20X%20to%20collection%200000024). + +## Ontologies + +The following table comes from Semantic Farm collection +[`0000024`](https://semantic.farm/collection/0000024), which is automatically +synced from the TIB Terminology Service collection +[`fairmat`](https://service.tib.eu/terminology/collections/fairmat). + +| Prefix | Name | License | +| ------------------------------------------ | ------------------------------------------ | --------- | +| [`BFO`](https://semantic.farm/bfo) | Basic Formal Ontology | CC-BY-4.0 | +| [`nexus`](https://semantic.farm/nexus) | NeXusOntology | | +| [`tfsco`](https://semantic.farm/tfsco) | Thin-film Solar Cells Ontology | | +| [`voc4cat`](https://semantic.farm/voc4cat) | A vocabulary for the catalysis disciplines | CC0-1.0 | + +## Colophon + +This page was automatically generated on 2026-05-07 using Semantic Farm +([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +by running the following commands: + +```console +$ git clone https://github.com/nfdi-de/nfdi-sections +$ cd nfdi-sections +$ uv run scripts/update_collections.py +$ git commit -am "Update WG Onto collections" +$ git push +``` diff --git a/docs/meta/wg_onto/used-ontologies/ghga.md b/docs/meta/wg_onto/used-ontologies/ghga.md index 9307b54..5b82bda 100644 --- a/docs/meta/wg_onto/used-ontologies/ghga.md +++ b/docs/meta/wg_onto/used-ontologies/ghga.md @@ -2,7 +2,49 @@ title: GHGA --- -Source: `/files/meta/Used_Ontologies_at_NFDI.xlsx` (sheet: GHGA) +A placeholder collection of ontologies, controlled vocabularies, and schemas +relevant for the GHGA Consortium created by the +[NFDI Section Metadata WG Ontology Harmonization and Mapping](https://github.com/nfdi-de/section-metadata-wg-onto/). +The working group is in the process of identifying GHGA Consortium members +appropriate for maintaining this collection. -|Ontology ID|Domain|License|Modularity|Format|developed / reused / only indexed / only evaluated|Used in| -|---|---|---|---|---|---|---| +## Maintainers + +- [Karoline Mauer](https://semantic.farm/orcid:0000-0002-9454-7941) + +Suggest a new addition to this collection +[here](https://github.com/biopragmatics/bioregistry/issues/new?template=add-collection-prefix.yml&collection=0000039&title=Add%20prefix%20X%20to%20collection%200000039). + +## Ontologies + +The following table comes from Semantic Farm collection +[`0000039`](https://semantic.farm/collection/0000039). + +| Prefix | Name | License | +| ---------------------------------------------- | -------------------------------------------- | ------------ | +| [`biolink`](https://semantic.farm/biolink) | BioLink Model | CC0-1.0 | +| [`COB`](https://semantic.farm/cob) | Core Ontology for Biology and Biomedicine | CC0-1.0 | +| [`DUO`](https://semantic.farm/duo) | Data Use Ontology | CC-BY-4.0 | +| [`edam`](https://semantic.farm/edam) | EDAM Ontology | CC-BY-SA-4.0 | +| [`EFO`](https://semantic.farm/efo) | Experimental Factor Ontology | Apache-2.0 | +| [`GENEPIO`](https://semantic.farm/genepio) | Genomic Epidemiology Ontology | CC-BY-3.0 | +| [`GHGA`](https://semantic.farm/ghga) | GHGA Metadata Schema | | +| [`GSSO`](https://semantic.farm/gsso) | Gender, Sex, and Sexual Orientation Ontology | Apache-2.0 | +| [`HANCESTRO`](https://semantic.farm/hancestro) | Human Ancestry Ontology | CC-BY-4.0 | +| [`linkml`](https://semantic.farm/linkml) | LinkML | | +| [`NCIT`](https://semantic.farm/ncit) | NCI Thesaurus | CC-BY-4.0 | +| [`SIO`](https://semantic.farm/sio) | Semanticscience Integrated Ontology | CC-BY-4.0 | + +## Colophon + +This page was automatically generated on 2026-05-07 using Semantic Farm +([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +by running the following commands: + +```console +$ git clone https://github.com/nfdi-de/nfdi-sections +$ cd nfdi-sections +$ uv run scripts/update_collections.py +$ git commit -am "Update WG Onto collections" +$ git push +``` diff --git a/docs/meta/wg_onto/used-ontologies/index.md b/docs/meta/wg_onto/used-ontologies/index.md index 097c1e8..c8bfe61 100644 --- a/docs/meta/wg_onto/used-ontologies/index.md +++ b/docs/meta/wg_onto/used-ontologies/index.md @@ -2,30 +2,73 @@ title: Used Ontologies --- -This section lists per-consortium ontology tables currently available in this folder. - -Pages: -- [BERD@NFDI](/docs/meta/wg_onto/used-ontologies/berd-nfdi) -- [common TLO concepts](/docs/meta/wg_onto/used-ontologies/common-tlo-concepts) -- [DataPLANT](/docs/meta/wg_onto/used-ontologies/dataplant) -- [FAIRagro](/docs/meta/wg_onto/used-ontologies/fairagro) -- [GHGA](/docs/meta/wg_onto/used-ontologies/ghga) -- [KonsortSWD](/docs/meta/wg_onto/used-ontologies/konsortswd) -- [MaRDI](/docs/meta/wg_onto/used-ontologies/mardi) -- [NFDI-MatWerk](/docs/meta/wg_onto/used-ontologies/nfdi-matwerk) -- [NFDI4Biodiversity](/docs/meta/wg_onto/used-ontologies/nfdi4biodiversity) -- [NFDI4BIOIMAGE](/docs/meta/wg_onto/used-ontologies/nfdi4bioimage) -- [NFDI4Cat](/docs/meta/wg_onto/used-ontologies/nfdi4cat) -- [NFDI4Chem](/docs/meta/wg_onto/used-ontologies/nfdi4chem) -- [NFDI4Culture](/docs/meta/wg_onto/used-ontologies/nfdi4culture) -- [NFDI4DataScience](/docs/meta/wg_onto/used-ontologies/nfdi4datascience) -- [NFDI4Earth](/docs/meta/wg_onto/used-ontologies/nfdi4earth) -- [NFDI4Energy](/docs/meta/wg_onto/used-ontologies/nfdi4energy) -- [NFDI4Health](/docs/meta/wg_onto/used-ontologies/nfdi4health) -- [NFDI4Immuno](/docs/meta/wg_onto/used-ontologies/nfdi4immuno) -- [NFDI4Ing](/docs/meta/wg_onto/used-ontologies/nfdi4ing) -- [NFDI4Memory](/docs/meta/wg_onto/used-ontologies/nfdi4memory) -- [NFDI4Microbiota](/docs/meta/wg_onto/used-ontologies/nfdi4microbiota) -- [NFDI4Objects](/docs/meta/wg_onto/used-ontologies/nfdi4objects) -- [NFDIxCS](/docs/meta/wg_onto/used-ontologies/nfdixcs) -- [Text+](/docs/meta/wg_onto/used-ontologies/text-plus) +The NFDI Section Metadata Working Group on Ontology Harmonization and Mapping +has generated an overview of the ontologies, terminologies, controlled +vocabularies, and related semantic artifacts used by each consortium. + +We first partnered with members of each consortium to collaboratively construct +their respective collections in the [Semantic Farm](https://semantic.farm), a +comprehensive registry of ontologies, terminologies, controlled vocabularies, +and related semantic artifacts. These collections can be iteratively extended by +following the "suggestion" link on one of the following pages, by making an +issue on the Semantic Farm's issue tracker, or by editing the underlying +[single source of truth JSON file](https://github.com/biopragmatics/bioregistry/blob/main/src/bioregistry/data/collections.json). + +:::note + +Some consortia use external systems for curating their ontology lists. For +example, NFDI4Chem curates their collection directly in the TIB-TS, +NFDI4Biodiversity has their own OntoPortal instance for which all loaded +ontologies comprise their collection, and NFDI4Objects curates their collection +in BARTOC. In these cases, the collections are synced into the Semantic Farm. +Each consortia's collection page gives additional context if it is maintained on +an external system. + +::: + +See source data at https://semantic.farm/collection/?ror=05qj6w324. + +## Consortia + +| Consortium | # | Collection Maintainers | +| ---------------------------------------------------------------------------- | --- | -------------------------------------------------------- | +| [BERD@NFDI](/docs/meta/wg_onto/used-ontologies/berd-nfdi.md) | 3 | Atif Latif, Fidan Limani | +| [DAPHNE4NFDI](/docs/meta/wg_onto/used-ontologies/daphne4nfdi.md) | 1 | Heike Görzig, Rolf Krahl | +| [DataPLANT](/docs/meta/wg_onto/used-ontologies/dataplant.md) | 39 | Angela Kranz, Hannah Dörpholz, Kathryn Dumschott | +| [FAIRagro](/docs/meta/wg_onto/used-ontologies/fairagro.md) | 23 | Gabriel Schneider | +| [FAIRmat](/docs/meta/wg_onto/used-ontologies/fairmat.md) | 4 | Markus Kühbach | +| [GHGA](/docs/meta/wg_onto/used-ontologies/ghga.md) | 12 | Karoline Mauer | +| [KonsortSWD](/docs/meta/wg_onto/used-ontologies/konsortswd.md) | 37 | Noemi Betancort | +| [MaRDI](/docs/meta/wg_onto/used-ontologies/mardi.md) | 8 | Björn Schembera | +| [NDFI4Cat](/docs/meta/wg_onto/used-ontologies/ndfi4cat.md) | 26 | Hendrik Borgelt, Alexander Behr, David Linke | +| [NFDI-MatWerk](/docs/meta/wg_onto/used-ontologies/nfdi-matwerk.md) | 6 | Ebrahim Nourouzi, Heike Fliegl | +| [NFDI4BIOIMAGE](/docs/meta/wg_onto/used-ontologies/nfdi4bioimage.md) | 22 | Damien Goutte-Gattat | +| [NFDI4Biodiversity](/docs/meta/wg_onto/used-ontologies/nfdi4biodiversity.md) | 65 | Naouel Karam, Ralph Schäfermeier | +| [NFDI4Chem](/docs/meta/wg_onto/used-ontologies/nfdi4chem.md) | 46 | Philip Strömert | +| [NFDI4Culture](/docs/meta/wg_onto/used-ontologies/nfdi4culture.md) | 30 | Tabea Tietz | +| [NFDI4DataScience](/docs/meta/wg_onto/used-ontologies/nfdi4datascience.md) | 3 | Benjamin Zapilko | +| [NFDI4Earth](/docs/meta/wg_onto/used-ontologies/nfdi4earth.md) | 27 | Auriol Degbelo | +| [NFDI4Energy](/docs/meta/wg_onto/used-ontologies/nfdi4energy.md) | 17 | Amanda Wein | +| [NFDI4Health](/docs/meta/wg_onto/used-ontologies/nfdi4health.md) | 38 | Matthias Löbe | +| [NFDI4Immuno](/docs/meta/wg_onto/used-ontologies/nfdi4immuno.md) | | Sebastian Böhm, Ulrik Stervbo | +| [NFDI4Ing](/docs/meta/wg_onto/used-ontologies/nfdi4ing.md) | 102 | Dorothea Iglezakis, Giacomo Lanza, Susanne Arndt | +| [NFDI4Memory](/docs/meta/wg_onto/used-ontologies/nfdi4memory.md) | 21 | Tabea Tietz | +| [NFDI4Microbiota](/docs/meta/wg_onto/used-ontologies/nfdi4microbiota.md) | | Anandhi Iyappan, Maja Magel, Noriko Cassman | +| [NFDI4Objects](/docs/meta/wg_onto/used-ontologies/nfdi4objects.md) | 47 | Anja Gerber, Florian Thiery, Jakob Voß, Kristina Fischer | +| [NFDIxCS](/docs/meta/wg_onto/used-ontologies/nfdixcs.md) | | Fabian Huch | +| [PUNCH4NFDI](/docs/meta/wg_onto/used-ontologies/punch4nfdi.md) | | Harry Enke | +| [Text+](/docs/meta/wg_onto/used-ontologies/text-plus.md) | 15 | Thorsten Trippel | + +## Colophon + +This page was automatically generated on 2026-05-07 using Semantic Farm +([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +by running the following commands: + +```console +$ git clone https://github.com/nfdi-de/nfdi-sections +$ cd nfdi-sections +$ uv run scripts/update_collections.py +$ git commit -am "Update WG Onto collections" +$ git push +``` diff --git a/docs/meta/wg_onto/used-ontologies/konsortswd.md b/docs/meta/wg_onto/used-ontologies/konsortswd.md index 737a3e9..f0c8b92 100644 --- a/docs/meta/wg_onto/used-ontologies/konsortswd.md +++ b/docs/meta/wg_onto/used-ontologies/konsortswd.md @@ -2,37 +2,74 @@ title: KonsortSWD --- -Source: `/files/meta/Used_Ontologies_at_NFDI.xlsx` (sheet: KonsortSWD) - -|Ontology ID|Domain|License|Modularity|Format|developed / reused / only indexed / only evaluated|Used in|Comments| -|---|---|---|---|---|---|---|---| -|MeSH|biomedical and health-related fields||Thesaurus from US National Library of Medicine, also in RDF, SPARQL|rdf|only indexed|PubMed, MEDLINE|Medical Subject Headings (MeSH) thesaurus| -|ISCO|International Standard Classifcation of Occupations|CC0 1.0|ISCED-ISCO, maps_to: "KldB"||only evaluated|International Labour Organization|| -|ISCED2011|International Standard Classification of Education||||only indexed|UNESCO, Statistisches Bundesamt|description of national educational systems and a methodology that translates national educational programmes into internationally comparable levels of education: education attainment| -|ISCED-F 2013|Fields of education and training 2013||||only indexed|UNESCO, Statistisches Bundesamt|| -|THESOZ|Social Sciences Thesaurus||SKOS (RDF), maps_to: "DBPEDIA, STW"|skos|only indexed|GESIS|(general) concepts, subjects and topics| -|STW|Economics|CC BY 4.0|SKOS (RDF), maps_to: "DBPEDIA, STW"|skos|only indexed|ZBW - Leibniz Information Centre for Economics : portal for economics EconBiz|vocabulary on any economic subject| -|TEI|Textual Documents||XML schema|xsd|only evaluated|internal use for the annotation of interview transcriptions, corpora|standard for the representation of texts in digital form| -|WIKIDATA|generic||||only evaluated||general concepts, subjects and topics| -|ISO-3166|Country codes||||only indexed|Statistisches Bundesamt, libraries, data portals, databases|authority control| -|ISO-639-3|Language codes||||only indexed|Statistisches Bundesamt, libraries, data portals, databases|authority control| -|GND|generic|||rdf|only indexed||authority control, general concepts, subjects and topics| -|Vocabulary of Demography|social sciences, demography, statistics||||only evaluated|IUSSP-CODATA Working Group on FAIR Vocabularies|work in progress| -|CESSDA/DDI Vocabularies|social sciences|CC BY 4.0|RDF: SKOS|skos|reused|CESSDA and DDI data archives|a detailed list will be added here| -|CESSDA|social sciences|CC BY-NC-SA 4.0||skos|reused||| -|Data Documentation Initiative (DDI)|social sciences, survey data|CC BY 4.0|XML schema|xsd|reused||abstract data model: it metadata about both quantitative and qualitative research data in the social, behavioral, economic, and health sciences| -|SDTL|variable-level data tranformation (statistical analysis), social sciences|CC BY 4.0|JSON and XML Schema, RDF/OWL, UML/XMI , DDI integration|owl|reused|statistical analysis processes/packages|integration of provenance metadata in DDI and other metadata standards| -|ELSST|social sciences|CC BY-SA 4.0||skos|only indexed|CESSDA|| -|CIDOC CRM|anthropology||XML, RDF|owl|only evaluated|CIDOC|not sure| -|Component Metadata Initiative (CMDI)|language resources||meta-model for the integration of metadata components (schemas)|xsd|only evaluated|CLARIN, AGD|framework to create and use self-defined metadata formats| -|Qualitative Data Model|qualitative data, qualitative methods (social sciences)|draft|abstract data model, UML||only evaluated|DDI qualitative data archives|not implemented yet| -|DDI-CDI|cross-domain|CC BY 4.0|Unified Modeling Language (UML) "Canonical XMI" form for easy use in other technology platforms|xsd|only evaluated|DDI Alliance|| -|QuDEx|qualitative data, qualitative methods (social sciences)|draft|XSD Schema|xsd|only evaluated|UK Data Archive|last updated 2014| -|REFI-QDA Standard|qualitative data, qualitative methods (social sciences)|MIT license, Copyright 2019 REFI www.qdasoftware.org|XSD Schema, UML|xsd|only evaluated|QDA-Software companies (Atlas.ti, MaxQDA...)|It enables interoperability between Qualitative Data Analysis Software (QDAS or CAQDAS) programs| -|Kernset Bildungsforschung|educational research|CC BY-SA 4.0|Application Profile for da-ra|xsd|only indexed|VerbundFDB|| -|da\|ra Metadata Schema|social sciences|CC0 1.0|XSD Schema|xsd|reused|GESIS, ZWB, DataCite|for DOI registration| -|XKOS|statistical classifications and concept management systems|CC BY 4.0|SKOS extension, RDF/OWL|owl|only evaluated|DDI data centers|an SKOS extension for representing statistical classifications| -|DUO|Data Use Ontology, biomedicine, genomics and health|CC BY 4.0|OBO_based|owl|only evaluated|ELIXIR, Charité|not sure| -|IAO|Information Artifact Ontology|CC BY 4.0|OBO_based|owl|only evaluated||not sure| -|ICO|Informed Consent Ontology, medical field|CC BY 3.0|OBO_based|owl|only evaluated||not sure| -|KonsortSWD Soziodemographische Standardvariablen|Social and health sciences (microdata on region of residence, date of birth, sex, citizenship, country of birth, education, main status, occupation, marital status...)|CC BY 4.0|uses AGS, NUTS, BEV-Codes der deutschen Staats- und Gebietssystematik (states and citizenships), Standard country or area codes for statistical use (M49), International Standard Classification of Occupations 2008 (ISCO) - deutsche Fassung, Klassifikation der Berufe 2010, EU key social variables, Demographische Standards||reused and developed|GESIS - ALLBUS, LIfBi - NEPS, various other national and international surveys and national and international official statistics|KonsortSWD service that reuses and, if necessary, develops and validates, coding schemes for sociodemographic variables in surveys to improve their (semantic/substantive) interoperability. Not sure whether each coding scheme needs to be regarded as an ontology/CV; given the multitude of variables covered, the service builds upon many existing classifications/ontologies. Many of these are available in various formats such as xml, json, markdown but I am not technically familiar with any of the formats mentioned here. There may be better sources than the ones I've found.| +[KonsortSWD (Strengthen, Widen, Deepen)](https://www.nfdi.de/consortia-konsortswd) +is the German National Data Infrastructure (NFDI) consortium for social, +educational, behavioral, and economic sciences. This collection reflects the +prefixes collected by NFDI Section Metadata for ontologies and controlled +vocabularies used by members of the consortium. + +## Maintainers + +- [Noemi Betancort](https://semantic.farm/orcid:0000-0002-0156-3556) + +Suggest a new addition to this collection +[here](https://github.com/biopragmatics/bioregistry/issues/new?template=add-collection-prefix.yml&collection=0000020&title=Add%20prefix%20X%20to%20collection%200000020). + +## Ontologies + +The following table comes from Semantic Farm collection +[`0000020`](https://semantic.farm/collection/0000020). + +| Prefix | Name | License | +| -------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------- | --------- | +| [`cessda`](https://semantic.farm/cessda) | Consortium of European Social Science Data Archives Vocabulary | | +| [`cessda.cdcpublishernames`](https://semantic.farm/cessda.cdcpublishernames) | CDC Publisher Names | CC-BY-4.0 | +| [`cessda.cessdadatacataloguecollections`](https://semantic.farm/cessda.cessdadatacataloguecollections) | CESSDA Data Catalogue Collections | CC-BY-4.0 | +| [`cessda.cessdapersistentidentifiertypes`](https://semantic.farm/cessda.cessdapersistentidentifiertypes) | CESSDA Persistent Identifier Types | CC-BY-4.0 | +| [`cessda.countrynamesandcodes`](https://semantic.farm/cessda.countrynamesandcodes) | Country Names and Codes | CC-BY-4.0 | +| [`cessda.topicclassification`](https://semantic.farm/cessda.topicclassification) | CESSDA Topic Classification | CC-BY-4.0 | +| [`ddi.aggregationmethod`](https://semantic.farm/ddi.aggregationmethod) | Aggregation Method | CC-BY-4.0 | +| [`ddi.analysisunit`](https://semantic.farm/ddi.analysisunit) | Analysis Unit | CC-BY-4.0 | +| [`ddi.characterset`](https://semantic.farm/ddi.characterset) | Character Set | CC-BY-4.0 | +| [`ddi.commonalitytype`](https://semantic.farm/ddi.commonalitytype) | Commonality Type | CC-BY-4.0 | +| [`ddi.contributorrole`](https://semantic.farm/ddi.contributorrole) | Contributor Role | CC-BY-4.0 | +| [`ddi.datasourcetype`](https://semantic.farm/ddi.datasourcetype) | Data Source Type | CC-BY-4.0 | +| [`ddi.datatype`](https://semantic.farm/ddi.datatype) | Data Type | CC-BY-4.0 | +| [`ddi.datetype`](https://semantic.farm/ddi.datetype) | Date Type | CC-BY-4.0 | +| [`ddi.generaldataformat`](https://semantic.farm/ddi.generaldataformat) | General Data Format | CC-BY-4.0 | +| [`ddi.languageproficiency`](https://semantic.farm/ddi.languageproficiency) | Language Proficiency | CC-BY-4.0 | +| [`ddi.lifecycleeventtype`](https://semantic.farm/ddi.lifecycleeventtype) | Lifecycle Event Type | CC-BY-4.0 | +| [`ddi.modeofcollection`](https://semantic.farm/ddi.modeofcollection) | Mode Of Collection | CC-BY-4.0 | +| [`ddi.numerictype`](https://semantic.farm/ddi.numerictype) | Numeric Type | CC-BY-4.0 | +| [`ddi.responseunit`](https://semantic.farm/ddi.responseunit) | Response Unit | CC-BY-4.0 | +| [`ddi.samplingprocedure`](https://semantic.farm/ddi.samplingprocedure) | Sampling Procedure | CC-BY-4.0 | +| [`ddi.softwarepackage`](https://semantic.farm/ddi.softwarepackage) | Software Package | CC-BY-4.0 | +| [`ddi.summarystatistictype`](https://semantic.farm/ddi.summarystatistictype) | Summary Statistic Type | CC-BY-4.0 | +| [`ddi.timemethod`](https://semantic.farm/ddi.timemethod) | Time Method | CC-BY-4.0 | +| [`ddi.timezone`](https://semantic.farm/ddi.timezone) | Time Zone | CC-BY-4.0 | +| [`ddi.typeofaddress`](https://semantic.farm/ddi.typeofaddress) | Type of Address | CC-BY-4.0 | +| [`ddi.typeofconceptgroup`](https://semantic.farm/ddi.typeofconceptgroup) | Type of Concept Group | CC-BY-4.0 | +| [`ddi.typeoffrequency`](https://semantic.farm/ddi.typeoffrequency) | Type of Frequency | CC-BY-4.0 | +| [`ddi.typeofinstrument`](https://semantic.farm/ddi.typeofinstrument) | Type of Instrument | CC-BY-4.0 | +| [`ddi.typeofnote`](https://semantic.farm/ddi.typeofnote) | Type of Note | CC-BY-4.0 | +| [`ddi.typeoftelephone`](https://semantic.farm/ddi.typeoftelephone) | Type of Telephone | CC-BY-4.0 | +| [`ddi.typeoftranslationmethod`](https://semantic.farm/ddi.typeoftranslationmethod) | Type of Translation Method | CC-BY-4.0 | +| [`gesis.kategorienschemawahlstudien`](https://semantic.farm/gesis.kategorienschemawahlstudien) | Category Scheme Election Studies | CC-BY-4.0 | +| [`gesis.rexconcepts`](https://semantic.farm/gesis.rexconcepts) | Central concepts of REX research | CC-BY-4.0 | +| [`gesis.rexdatatype`](https://semantic.farm/gesis.rexdatatype) | Data types in REX research | CC-BY-4.0 | +| [`gesis.rexgroups`](https://semantic.farm/gesis.rexgroups) | Diversification criteria of REX research | CC-BY-4.0 | +| [`gesis.variables-relations`](https://semantic.farm/gesis.variables-relations) | Variables relations for Social Sciences research data | CC-BY-4.0 | + +## Colophon + +This page was automatically generated on 2026-05-07 using Semantic Farm +([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +by running the following commands: + +```console +$ git clone https://github.com/nfdi-de/nfdi-sections +$ cd nfdi-sections +$ uv run scripts/update_collections.py +$ git commit -am "Update WG Onto collections" +$ git push +``` diff --git a/docs/meta/wg_onto/used-ontologies/mardi.md b/docs/meta/wg_onto/used-ontologies/mardi.md index 1d892cb..de3ccc5 100644 --- a/docs/meta/wg_onto/used-ontologies/mardi.md +++ b/docs/meta/wg_onto/used-ontologies/mardi.md @@ -2,15 +2,45 @@ title: MaRDI --- -Source: `/files/meta/Used_Ontologies_at_NFDI.xlsx` (sheet: MaRDI) - -|Ontology ID|Ontology name|Domain|License|Modularity|Format|developed / reused / only indexed / only evaluated|Used in|Comments|NFDI contributions| -|---|---|---|---|---|---|---|---|---|---| -|AlgoData|Algorithm Knowledge Graph Ontology|Ontology of mathematicals algorithms|||owl|developed|AlgoData|wip|| -|MathModDB|Ontology for Mathematical Models|Ontology of mathematical models|||owl|developed|Knowledge Graph for mathematical models|wip|| -|QUDT|Quantities, Units, Dimensons, Types|Quantities||||reused|MathModDB||| -|MSC|Mathematical Subject Classification|Application Domain|||skos|only evaluated|MathModDB||| -|PhysSH|Physical Subject Classification|Application Domain||||only evaluated|MathModDB||| -|Basisklassifikation||Application Domain||||only evaluated|MathModDB||| -|CodeMeta||Software||||only evaluated|||| -|AMV|Algorithms Metadata Vocabulary|||||only evaluated|||| +A placeholder collection of ontologies, controlled vocabularies, and schemas +relevant for the MaRDI Consortium created by the +[NFDI Section Metadata WG Ontology Harmonization and Mapping](https://github.com/nfdi-de/section-metadata-wg-onto/). +The working group is in the process of identifying MaRDI Consortium members +appropriate for maintaining this collection. + +## Maintainers + +- [Björn Schembera](https://semantic.farm/orcid:0000-0003-2860-6621) + +Suggest a new addition to this collection +[here](https://github.com/biopragmatics/bioregistry/issues/new?template=add-collection-prefix.yml&collection=0000027&title=Add%20prefix%20X%20to%20collection%200000027). + +## Ontologies + +The following table comes from Semantic Farm collection +[`0000027`](https://semantic.farm/collection/0000027). + +| Prefix | Name | License | +| ------------------------------------------------ | -------------------------------------------------------------- | --------------- | +| [`amv`](https://semantic.farm/amv) | Algorithm Metadata Vocabulary | CC0-1.0 | +| [`codemeta`](https://semantic.farm/codemeta) | CodeMeta | Apache-2.0 | +| [`mathalgodb`](https://semantic.farm/mathalgodb) | Algorithm Knowledge Graph Ontology | CC-BY-4.0 | +| [`mathmoddb`](https://semantic.farm/mathmoddb) | MathModDB Ontology and Knowledge Graph for Mathematical Models | CC-BY-4.0 | +| [`msc`](https://semantic.farm/msc) | Mathematics Subject Classification | CC-BY-NC-SA-3.0 | +| [`physh`](https://semantic.farm/physh) | Physics Subject Headings | CC0-1.0 | +| [`qudt`](https://semantic.farm/qudt) | Quantities, Units, Dimensions, and Types Ontology | CC-BY-4.0 | +| [`tib.bk`](https://semantic.farm/tib.bk) | Basic Classification | CC0-1.0 | + +## Colophon + +This page was automatically generated on 2026-05-07 using Semantic Farm +([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +by running the following commands: + +```console +$ git clone https://github.com/nfdi-de/nfdi-sections +$ cd nfdi-sections +$ uv run scripts/update_collections.py +$ git commit -am "Update WG Onto collections" +$ git push +``` diff --git a/docs/meta/wg_onto/used-ontologies/ndfi4cat.md b/docs/meta/wg_onto/used-ontologies/ndfi4cat.md new file mode 100644 index 0000000..367711a --- /dev/null +++ b/docs/meta/wg_onto/used-ontologies/ndfi4cat.md @@ -0,0 +1,74 @@ +--- +title: NDFI4Cat +--- + +A collection of ontologies, controlled vocabularies, and schemas relevant for +the NDFI4Cat Consortium. + +This collection was originally based on the metadata landscape of the ontologies +in this list can be found +[here](https://github.com/nfdi4cat/Ontology-Overview-of-NFDI4Cat). + +OntoCompChem and OntoKin appear on the NFDI4Cat list but have not yet been +registered in the Bioregistry because the resources are missing/incomplete such +that they do not meet minimum Bioregistry metadata standards. These might be +added in the future if additional metadata can be found. + +## Maintainers + +- [Hendrik Borgelt](https://semantic.farm/orcid:0000-0001-5886-7860) +- [Alexander Behr](https://semantic.farm/orcid:0000-0003-4620-8248) +- [David Linke](https://semantic.farm/orcid:0000-0002-5898-1820) + +Suggest a new addition to this collection +[here](https://github.com/biopragmatics/bioregistry/issues/new?template=add-collection-prefix.yml&collection=0000011&title=Add%20prefix%20X%20to%20collection%200000011). + +## Ontologies + +The following table comes from Semantic Farm collection +[`0000011`](https://semantic.farm/collection/0000011), which is automatically +synced from the TIB Terminology Service collection +[`nfdi4cat`](https://service.tib.eu/terminology/collections/nfdi4cat). + +| Prefix | Name | License | +| -------------------------------------------------------------------- | ------------------------------------------------------------- | --------------------------------------------------- | +| [`afo`](https://semantic.farm/afo) | Allotrope Merged Ontology Suite | [Custom](http://purl.allotrope.org/voc/copyright) | +| [`bao`](https://semantic.farm/bao) | BioAssay Ontology | CC-BY-SA-4.0 | +| [`BFO`](https://semantic.farm/bfo) | Basic Formal Ontology | CC-BY-4.0 | +| [`cao`](https://semantic.farm/cao) | Chemical Analysis Ontology | CC-BY-3.0 | +| [`CHEBI`](https://semantic.farm/chebi) | Chemical Entities of Biological Interest | CC-BY-4.0 | +| [`CHEMINF`](https://semantic.farm/cheminf) | Chemical Information Ontology | CC0-1.0 | +| [`CHMO`](https://semantic.farm/chmo) | Chemical Methods Ontology | CC-BY-4.0 | +| [`dolce`](https://semantic.farm/dolce) | Descriptive Ontology for Linguistic and Cognitive Engineering | | +| [`edam`](https://semantic.farm/edam) | EDAM Ontology | CC-BY-SA-4.0 | +| [`emmo`](https://semantic.farm/emmo) | Elementary Multiperspective Material Ontology | CC-BY-4.0 | +| [`emmo.cif`](https://semantic.farm/emmo.cif) | Crystallographic Information Framework | | +| [`ENVO`](https://semantic.farm/envo) | Environment Ontology | CC0-1.0 | +| [`iso15926`](https://semantic.farm/iso15926) | ISO 15926-14 | | +| [`m4i`](https://semantic.farm/m4i) | Metadata4Ing | CC-BY-4.0 | +| [`MOP`](https://semantic.farm/mop) | Molecular Process Ontology | CC-BY-4.0 | +| [`MS`](https://semantic.farm/ms) | Mass spectrometry ontology | CC-BY-3.0 | +| [`OBI`](https://semantic.farm/obi) | Ontology for Biomedical Investigations | CC-BY-4.0 | +| [`om`](https://semantic.farm/om) | Ontology of units of Measure | CC-BY-4.0 | +| [`ontocape`](https://semantic.farm/ontocape) | Ontology for computer aided process engineering | GPL-2.0 | +| [`osmo`](https://semantic.farm/osmo) | Ontology for simulation, modelling, and optimization | [Custom](http://rightsstatements.org/vocab/InC/1.0) | +| [`REX`](https://semantic.farm/rex) | Physico-chemical process | | +| [`RXNO`](https://semantic.farm/rxno) | Name Reaction Ontology | CC-BY-4.0 | +| [`SBO`](https://semantic.farm/sbo) | Systems Biology Ontology | Artistic-2.0 | +| [`voc4cat`](https://semantic.farm/voc4cat) | A vocabulary for the catalysis disciplines | CC0-1.0 | +| [`worldavatar.compchem`](https://semantic.farm/worldavatar.compchem) | Computational Chemistry Ontology | | +| [`worldavatar.kin`](https://semantic.farm/worldavatar.kin) | Ontology for Chemical Kinetic Reaction Mechanisms | | + +## Colophon + +This page was automatically generated on 2026-05-07 using Semantic Farm +([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +by running the following commands: + +```console +$ git clone https://github.com/nfdi-de/nfdi-sections +$ cd nfdi-sections +$ uv run scripts/update_collections.py +$ git commit -am "Update WG Onto collections" +$ git push +``` diff --git a/docs/meta/wg_onto/used-ontologies/nfdi-matwerk.md b/docs/meta/wg_onto/used-ontologies/nfdi-matwerk.md index df10a20..50fcc09 100644 --- a/docs/meta/wg_onto/used-ontologies/nfdi-matwerk.md +++ b/docs/meta/wg_onto/used-ontologies/nfdi-matwerk.md @@ -2,18 +2,42 @@ title: NFDI-MatWerk --- -Source: `/files/meta/Used_Ontologies_at_NFDI.xlsx` (sheet: NFDI-MatWerk) - -|Ontology ID|Domain|License|Modularity|Format|developed / reused / only indexed / only evaluated|Used in|Comment| -|---|---|---|---|---|---|---|---| -|MDMC-NEP|top-level management of research experiments workflow|CC BY 3.0|based on the MDMC Glossary and aligned with PROV-O, DCTERM for annotations||reused|JL MDMC, NEP, EOSC-Pillar|https://jl-mdmc-helmholtz.de/ontology/; https://github.com/Materials-Data-Science-and-Informatics/MDMC-NEP-top-level-ontology| -|user schema|||||reused|JL MDMC, NEP, MatWerk|| -|sample schema|physical samples||||reused|JL MDMC, NEP|| -|SEM schema|Scanning Electron Microscopy||user, sample||reused|JL MDMC, NEP, MatWerk|| -|TEM schema|Transmission Electron Microscopy||user, sample||reused|JL MDMC, NEP|| -|MRI schema|Magnetic Resonance Imaging||user||reused|JL MDMC, NEP, HMC|| -|MWO|research information about the NFDI-MatWerk|CC BY 4.0|based on NFDICO, imports SCHEMA, maps_to: "DCAT, DOAP, FOAF, FABIO, SD, VCARD, VIVO, SWO, WIKIDATA, ORG, FRAPO, MODSCI, DBO, SCHEMA, DCTERMS, IAO, OBI"|owl|extended existing modular ontologies|MatWerk|based on NFDICO, see https://ise-fizkarlsruhe.github.io/nfdicore/| -|NFDICORE||||owl|||| -|PMD|Material Science|||owl||Platform Materail Digital|https://w3id.org/pmd/co/| -|Chebi|Chemistry|||owl|||| -|BFO2020||||owl|||| +A collection of ontologies, controlled vocabularies, and schemas relevant for +the NFDI-MatWerk Consortium created in cooperation with the +[NFDI Section Metadata WG Ontology Harmonization and Mapping](https://github.com/nfdi-de/section-metadata-wg-onto/). + +## Maintainers + +- [Ebrahim Nourouzi](https://semantic.farm/orcid:0000-0002-2691-6995) +- [Heike Fliegl](https://semantic.farm/orcid:0000-0002-7541-115X) + +Suggest a new addition to this collection +[here](https://github.com/biopragmatics/bioregistry/issues/new?template=add-collection-prefix.yml&collection=0000031&title=Add%20prefix%20X%20to%20collection%200000031). + +## Ontologies + +The following table comes from Semantic Farm collection +[`0000031`](https://semantic.farm/collection/0000031). + +| Prefix | Name | License | Comment | +| ---------------------------------------------- | ----------------------------------------------------- | --------- | --------------------------------- | +| [`BFO`](https://semantic.farm/bfo) | Basic Formal Ontology | CC-BY-4.0 | | +| [`CHEBI`](https://semantic.farm/chebi) | Chemical Entities of Biological Interest | CC-BY-4.0 | | +| [`mwo`](https://semantic.farm/mwo) | NFDI MatWerk Ontology | CC0-1.0 | | +| [`nfdi.core`](https://semantic.farm/nfdi.core) | NFDI Core Ontology | CC0-1.0 | | +| [`pmdco`](https://semantic.farm/pmdco) | Platform Material Digital Core Ontology | CC-BY-4.0 | | +| [`prima`](https://semantic.farm/prima) | Provenance Information for Materials Science Ontology | CC-BY-3.0 | used by JL MDMC, NEP, EOSC-Pillar | + +## Colophon + +This page was automatically generated on 2026-05-07 using Semantic Farm +([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +by running the following commands: + +```console +$ git clone https://github.com/nfdi-de/nfdi-sections +$ cd nfdi-sections +$ uv run scripts/update_collections.py +$ git commit -am "Update WG Onto collections" +$ git push +``` diff --git a/docs/meta/wg_onto/used-ontologies/nfdi4biodiversity.md b/docs/meta/wg_onto/used-ontologies/nfdi4biodiversity.md index 03d94cc..e418f32 100644 --- a/docs/meta/wg_onto/used-ontologies/nfdi4biodiversity.md +++ b/docs/meta/wg_onto/used-ontologies/nfdi4biodiversity.md @@ -2,31 +2,103 @@ title: NFDI4Biodiversity --- -Source: `/files/meta/Used_Ontologies_at_NFDI.xlsx` (sheet: NFDI4Biodiversity) - -|Ontology ID|Ontology|Domain|License|Format|developed / reused / only indexed / only evaluated|Modularity|GFbio|Obofoundry|OLS URL|Bioportal|Github|File URL|Other URL|Description| |Useful Links:|OBO Foundry|NCBO BioPortal|OLS ontology search|GFBio Terminology Service| -|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---| -|BCO|Biological Collections Ontology|biology|CC0 1.0|owl|reused|BFO|https://terminologies.gfbio.org/terminology/BCO|https://obofoundry.org/ontology/bco.html|https://www.ebi.ac.uk/ols/ontologies/bco|https://bioportal.bioontology.org/ontologies/BCO|https://github.com/BiodiversityOntologies/bco|https://bioportal.bioontology.org/ontologies/BCO||The biological collection ontology includes consideration of the distinctions between individuals, organisms, voucher specimens, lots, and samples the relations between these entities, and processes governing the creation and use of "samples". Within scope as well are properties including collector, location, time, storage environment, containers, institution, and collection identifiers.||Comments:|Please (also) check out the DataPlant sheet, there is some overlap ... Gruss, Steffen|||| -|CHEBI|Chemical Entities of Biological Interest Ontology|chemistry|CC BY 4.0|owl|reused||https://terminologies.gfbio.org/terminology/CHEBI|https://obofoundry.org/ontology/chebi.html|https://www.ebi.ac.uk/ols/ontologies/chebi|https://bioportal.bioontology.org/ontologies/CHEBI|https://github.com/ebi-chebi/ChEBI|https://bioportal.bioontology.org/ontologies/CHEBI|http://www.ebi.ac.uk/chebi|A structured classification of chemical compounds of biological relevance.| -|ENVO|Environment Ontology|environmental|CC0 1.0|owl|reused|BFO|https://terminologies.gfbio.org/terminology/ENVO|https://obofoundry.org/ontology/envo.html|https://www.ebi.ac.uk/ols/ontologies/envo|https://bioportal.bioontology.org/ontologies/ENVO|https://github.com/EnvironmentOntology/envo|https://raw.githubusercontent.com/EnvironmentOntology/envo/master/envo.owl|http://environmentontology.org/|The most up-to-date information about ENVO is available here: http://www.obofoundry.org/ontology/envo.html EnvO is an OBO Foundry and Library ontology for the concise, controlled description of environmental entities such as ecosystems, environmental processes, and environmental qualities. It closely interoperates with a broad collection of other OBO ontologies and is used in a diverse range of projects.| -|FLOPO|Flora Phenotype Ontology|anatomical|CC BY 3.0|owl|reused||https://terminologies.gfbio.org/terminology/FLOPOO|https://obofoundry.org/ontology/flopo.html|https://www.ebi.ac.uk/ols/ontologies/flopo|https://bioportal.bioontology.org/ontologies/FLOPO|https://github.com/flora-phenotype-ontology/flopoontology|https://github.com/flora-phenotype-ontology/flopoontology/tree/master/ontology||The Flora Phenotype Ontology is an ontology of phenotypes reported in Floras. The original version was developed at the pro-iBiosphere Hackathon in Leiden. This is the pre-classified version of the ontology; the original OWL file is at https://github.com/flora-phenotype-ontology/flopoontology/blob/master/ontology/flopo.owl The Flora Phenotype Ontology is generated from the Flora Malesiana, Flora Gabon, Flora of Central Africa, and a collection of Kews African Floras. Every class in the ontology has at least one taxon annotation. The (draft) taxon annotation are available at http://jagannath.pdn.cam.ac.uk/plant/flora/clean-rerun/| -|NCBITAXON|National Center for Biotechnology Information Organismal Classification|biology|CC0 1.0|owl|reused|OIO, DCTERMS, IAO|https://terminologies.gfbio.org/terminology/NCBITAXON|https://obofoundry.org/ontology/ncbitaxon.html|https://www.ebi.ac.uk/ols/ontologies/ncbitaxon|https://bioportal.bioontology.org/ontologies/NCBITAXON|https://github.com/obophenotype/ncbitaxon|https://bioportal.bioontology.org/ontologies/NCBITAXON|https://www.ncbi.nlm.nih.gov/taxonomy|The NCBI Taxonomy Database is a curated classification and nomenclature for all of the organisms in the public sequence databases.| -|OBOE|The Extensible Observation Ontology|environmental|CC BY 3.0|owl|reused||https://terminologies.gfbio.org/terminology/OBOE|||https://bioportal.bioontology.org/ontologies/OBOE|https://github.com/NCEAS/oboe|https://bioportal.bioontology.org/ontologies/OBOE||The Extensible Observation Ontology (OBOE) is a formal ontology for capturing the semantics of scientific observation and measurement. The ontology supports researchers to add detailed semantic annotations to scientific data, thereby clarifying the inherent meaning of scientific observations.| -|PATO|Phenotypic Quality Ontology|anatomical|CC BY 3.0|owl|reused|BFO|https://terminologies.gfbio.org/terminology/PATO|https://obofoundry.org/ontology/pato.html|https://www.ebi.ac.uk/ols/ontologies/pato|https://bioportal.bioontology.org/ontologies/PATO|https://github.com/pato-ontology/pato/|https://bioportal.bioontology.org/ontologies/PATO||Phenotypic qualities (properties). This ontology can be used in conjunction with other ontologies such as GO or anatomical ontologies to refer to phenotypes. Examples of qualities are red, ectopic, high temperature, fused, small, edematous and arrested.| -|PO|Plant Ontology|biology|CC BY 4.0|owl|reused|BFO|https://terminologies.gfbio.org/terminology/PO|https://obofoundry.org/ontology/po.html|https://www.ebi.ac.uk/ols/ontologies/po|https://bioportal.bioontology.org/ontologies/PO|https://github.com/Planteome/plant-ontology|https://bioportal.bioontology.org/ontologies/PO||The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data.| -|PTO|Plant Trait Ontology|anatomical|CC BY 4.0|owl|reused|BFO|https://terminologies.gfbio.org/terminology/PTO|https://obofoundry.org/ontology/to.html|https://www.ebi.ac.uk/ols/ontologies/to|https://bioportal.bioontology.org/ontologies/PTO|https://github.com/Planteome/plant-trait-ontology|https://bioportal.bioontology.org/ontologies/PTO||A controlled vocabulary to describe phenotypic traits in plants. Each trait is a distinguishable feature, characteristic, quality or phenotypic feature of a developing or mature plant, or a plant part.| -|QUDT|Quantity, Unit, Dimension and Type|other|CC BY 4.0|owl|reused|OBO_compatible|https://terminologies.gfbio.org/terminology/QUDT|||https://bioportal.bioontology.org/ontologies/QUDT|https://github.com/qudt/qudt-public-repo|https://github.com/qudt/qudt-public-repo/releases||The QUDT collection of ontologies define the base classes properties, and restrictions used for modeling physical quantities, units of measure, and their dimensions in various measurement systems. The goal of the QUDT ontology is to provide a unified model of, measurable quantities, units for measuring different kinds of quantities, the numerical values of quantities in different units of measure and the data structures and data types used to store and manipulate these objects in software. This OWL schema is a foundation for a basic treatment of units.| -|SWEET|Semantic Web for Earth and Environment Technology Ontology|geo-sciences|CC0 1.0|owl|reused||https://terminologies.gfbio.org/terminology/SWEET|||https://bioportal.bioontology.org/ontologies/SWEET|https://github.com/ESIPFed/sweet|https://bioportal.bioontology.org/ontologies/SWEET||| -|ETS|Ecological Trait-data Standard|biology|CC BY 4.0|owl|reused||https://terminologies.gfbio.org/terminology/ETS||||https://github.com/EcologicalTraitData/ETS|https://terminologies.gfbio.org/terms/ets/pages/||The Ecological Trait-data Standard defines terms for the use in datasets containing quantitative and qualitative functional traits.| -|RECORDBASIS|GFBio Agreed Vocabulary for RecordBasis|biology|CC0 1.0|owl|reused||https://terminologies.gfbio.org/terminology/RECORDBASIS|||||https://terminologies.gfbio.org/terms/recordbasis/||A controlled vocabulary (Terminology) "BasisOfRecords" or "RecordBasis" (DwC: "The specific nature of the data record."). Based on GBIF/ DwC and BiNHum/ABCD.| -|BOHLMANN|Bohlmann Ontology|biology|CC0 1.0|owl|reused||https://terminologies.gfbio.org/terminology/BOHLMANN|||||https://terminologies.gfbio.org/terms/bohlmann/||An ontology listing the natural substances that occurr in the plant family of Compositae (Asteraceae).| -|TRICHOPTERA|Trichoptera Ontology|biology||owl|reused||https://terminologies.gfbio.org/terminology/TRICHOPTERA|||||||Working list: taxon names of the order Trichoptera (caddisflies; Insecta).| -|THYSANOPTERA|Thysanoptera Ontology|biology||owl|reused||https://terminologies.gfbio.org/terminology/THYSANOPTERA|||||||Working list: taxon names of the order Thysanoptera (Insecta).| -|RIVERS_DE|German River Names|geo-sciences|GeoNutzV|owl|reused||https://terminologies.gfbio.org/terminology/RIVERS_DE|||||https://terminologies.gfbio.org/terms/rivers_de/||A controlled vocabulary of the names of rivers in Germany and their connections, extracted from the Shape File provided by the environmental authority of the Federal Republic of Germany: Umweltbundesamt (UBA).| -|ITIS|Integrated Taxonomic Information System|biology|CC0 1.0|owl|reused||https://terminologies.gfbio.org/terminology/ITIS||||||https://www.itis.gov/; https://www.gbif.org/dataset/9ca92552-f23a-41a8-a140-01abaa31c931|The White House Subcommittee on Biodiversity and Ecosystem Dynamics has identified systematics as a research priority that is fundamental to ecosystem management and biodiversity conservation. This primary need identified by the Subcommittee requires improvements in the organization of, and access to, standardized nomenclature. ITIS (originally referred to as the Interagency Taxonomic Information System) was designed to fulfill these requirements. In the future, the ITIS will provide taxonomic data and a directory of taxonomic expertise that will support the system. The ITIS is the result of a partnership of federal agencies formed to satisfy their mutual needs for scientifically credible taxonomic information. Since its inception, ITIS has gained valuable new partners and undergone a name change; ITIS now stands for the Integrated Taxonomic Information System.| -|KINGDOM|Kingdom Ontology|biology|CC0 1.0|owl|reused||https://terminologies.gfbio.org/terminology/KINGDOM|||||https://terminologies.gfbio.org/terms/kingdom||A controlled vocabulary (Terminology) for biological taxa "Higher Classification - Kingdom (=Regnum)". Based on GBIF and CoL.| -|ORIBATIDA|Oribatida Ontology|biology|CC0 1.0|owl|reused||https://terminologies.gfbio.org/terminology/ORIBATIDA|||||https://terminologies.gfbio.org/terms/oribatida/||Working list: taxon names of the order Oribatida (moss- or beetle-mites).| -|IHO|IHO World Seas|geo-sciences|CC BY 4.0|owl|reused|imports GEO and GEONAMES|https://terminologies.gfbio.org/terminology/IHO|||||https://terminologies.gfbio.org/terms/iho/|https://www.marineregions.org/sources.php#iho|A hierarchy of the world oceans, seas and sea regions, based on the publication "Limits of Oceans & Seas, Special Publication No. 23" (1953) by the International Hydrographic Organization (IHO), extracted from the Shape Files (version 2 [2017]) available on http://www.marineregions.org and provided by Flanders Marine Institute (VLIZ).| -|GEONAMES|The Geonames geographical database|geo-sciences|CC BY 4.0|owl|reused||https://terminologies.gfbio.org/terminology/GEONAMES|||||https://www.geonames.org/ontology/ontology_v3.3.rdf|http://www.geonames.org/|The GeoNames geographical database is available for download free of charge under a creative commons attribution license. It contains over 10 million geographical names and consists of over 9 million unique features whereof 2.8 million populated places and 5.5 million alternate names. All features are categorized into one out of nine feature classes and further subcategorized into one out of 645 feature codes. Only information from Germany is available right now.| -|ISOCOUNTRIES|ISO3166 Countries and Subdivisions|general|MIT|owl|reused||https://terminologies.gfbio.org/terminology/ISOCOUNTRIES|||||https://www.omg.org/spec/LCC/Countries/ISO3166-1-CountryCodes/|https://databus.dbpedia.org/ontologies/omg.org/spec--LCC--Countries--ISO3166-1-CountryCodes/2021.04.19-031153|A thersaurus of countries (ISO 3166-1) and country subdivisions (ISO 3166-2) with labels and alternative names in various languages, hierarchical connections between regions and subregions, and links to Wikidata and Geonames.| -|LIT_I|The lithologs rock names ontology for igneous rocks|geo-sciences|ODbL v1.0|skos|reused||https://terminologies.gfbio.org/terminology/LIT_I|||||http://www.lithologs.net/skos/igneous_rocks/all||The lithologs ontology for igneous rocks provides SKOSified information on the classification of igneous rocks extracted from the IUGS recommendations published by Le Maitre (ed.)(2002): Igneous rocks: a classification and glossary of terms| +A placeholder collection of ontologies, controlled vocabularies, and schemas +relevant for the NFDI4Biodiversity Consortium created by the +[NFDI Section Metadata WG Ontology Harmonization and Mapping](https://github.com/nfdi-de/section-metadata-wg-onto/). +The working group is in the process of identifying NFDI4Biodiversity Consortium +members appropriate for maintaining this collection. + +## Maintainers + +- [Naouel Karam](https://semantic.farm/orcid:0000-0002-6762-6417) +- [Ralph Schäfermeier](https://semantic.farm/orcid:0000-0002-4349-6726) + +Suggest a new addition to this collection +[here](https://github.com/biopragmatics/bioregistry/issues/new?template=add-collection-prefix.yml&collection=0000040&title=Add%20prefix%20X%20to%20collection%200000040). + +## Ontologies + +The following table comes from Semantic Farm collection +[`0000040`](https://semantic.farm/collection/0000040). + +| Prefix | Name | License | +| -------------------------------------------------------------- | -------------------------------------------------------------------- | --------------------------------------------------------------------------------- | +| [`abcd`](https://semantic.farm/abcd) | AntiBodies Chemically Defined database | CC-BY-4.0 | +| [`ahol`](https://semantic.farm/ahol) | Animal Health Ontology for Livestock | CC-BY-4.0 | +| [`AISM`](https://semantic.farm/aism) | Ontology for the Anatomy of the Insect SkeletoMuscular system | CC-BY-4.0 | +| [`APTO`](https://semantic.farm/apto) | Agriculture Product Types Ontology | CC-BY-4.0 | +| [`atol`](https://semantic.farm/atol) | Animal Trait Ontology for Livestock | CC-BY-4.0 | +| [`BCO`](https://semantic.farm/bco) | Biological Collections Ontology | CC0-1.0 | +| [`BFO`](https://semantic.farm/bfo) | Basic Formal Ontology | CC-BY-4.0 | +| [`biodivthes`](https://semantic.farm/biodivthes) | Biodiversity Thesaurus | CC-BY-4.0 | +| [`bohlmann`](https://semantic.farm/bohlmann) | Bohlmann Ontology | CC0-1.0 | +| [`BSPO`](https://semantic.farm/bspo) | Biological Spatial Ontology | CC-BY-3.0 | +| [`CARO`](https://semantic.farm/caro) | Common Anatomy Reference Ontology | CC-BY-4.0 | +| [`CHEBI`](https://semantic.farm/chebi) | Chemical Entities of Biological Interest | CC-BY-4.0 | +| [`CL`](https://semantic.farm/cl) | Cell Ontology | CC-BY-4.0 | +| [`COB`](https://semantic.farm/cob) | Core Ontology for Biology and Biomedicine | CC0-1.0 | +| [`codata.rdmt`](https://semantic.farm/codata.rdmt) | CODATA Research Data Management Terminology | CC-BY-4.0 | +| [`COLAO`](https://semantic.farm/colao) | Coleoptera Anatomy Ontology | CC-BY-4.0 | +| [`dcat`](https://semantic.farm/dcat) | Data Catalog | CC-BY-4.0 | +| [`dfg.fo`](https://semantic.farm/dfg.fo) | DFG Classification of Subject Areas Ontology - 2020-2024 | CC-BY-4.0 | +| [`ECO`](https://semantic.farm/eco) | Evidence and Conclusion Ontology | CC0-1.0 | +| [`edam`](https://semantic.farm/edam) | EDAM Ontology | CC-BY-SA-4.0 | +| [`ENVO`](https://semantic.farm/envo) | Environment Ontology | CC0-1.0 | +| [`envthes`](https://semantic.farm/envthes) | Thesaurus for long-term ecological research, monitoring, experiments | CC-BY-4.0 | +| [`eol`](https://semantic.farm/eol) | Environment Ontology for Livestock | CC-BY-4.0 | +| [`FLOPO`](https://semantic.farm/flopo) | Flora Phenotype Ontology | CC0-1.0 | +| [`geonames`](https://semantic.farm/geonames) | GeoNames | CC-BY-4.0 | +| [`gfbio.biobank`](https://semantic.farm/gfbio.biobank) | AMMOD Metabarcoding Ontology | | +| [`gfbio.biol`](https://semantic.farm/gfbio.biol) | Biological Taxonomy Vocabulary 0.2 (Core) | | +| [`gfbio.botany`](https://semantic.farm/gfbio.botany) | Biological Taxonomy Vocabulary 0.2 (Botany) | | +| [`gfbio.ets`](https://semantic.farm/gfbio.ets) | Ecological Trait-data Standard | CC-BY-4.0 | +| [`gfbio.iho`](https://semantic.farm/gfbio.iho) | IHO World Seas | | +| [`gfbio.kingdom`](https://semantic.farm/gfbio.kingdom) | Kingdom Ontology | CC0-1.0 | +| [`gfbio.top`](https://semantic.farm/gfbio.top) | Thesaurus of Plant Characteristics | | +| [`iadopt`](https://semantic.farm/iadopt) | I-ADOPT Framework Ontology | CC-BY-4.0 | +| [`inbio`](https://semantic.farm/inbio) | Invasion Biology Ontology | CC-BY-NC-SA-4.0 | +| [`iso.3166`](https://semantic.farm/iso.3166) | ISO 3166-1 Country Code | | +| [`itis`](https://semantic.farm/itis) | Integrated Taxonomic Information System | CC0-1.0 | +| [`LEPAO`](https://semantic.farm/lepao) | Lepidoptera Anatomy Ontology | CC-BY-4.0 | +| [`lpt`](https://semantic.farm/lpt) | Livestock Product Trait Ontology | CC-BY-4.0 | +| [`NCBITaxon`](https://semantic.farm/ncbitaxon) | NCBI Taxonomy | CC0-1.0 | +| [`nfdi.core`](https://semantic.farm/nfdi.core) | NFDI Core Ontology | CC0-1.0 | +| [`OBA`](https://semantic.farm/oba) | Ontology of Biological Attributes | CC0-1.0 | +| [`oboe`](https://semantic.farm/oboe) | The Extensible Observation Ontology | CC-BY-3.0 | +| [`odm2.methodtype`](https://semantic.farm/odm2.methodtype) | Method Type Vocabulary | | +| [`odm2.specimentype`](https://semantic.farm/odm2.specimentype) | Specimen Type Vocabulary | | +| [`oim`](https://semantic.farm/oim) | Ocean Information Model | CC-BY-4.0 | +| [`om`](https://semantic.farm/om) | Ontology of units of Measure | CC-BY-4.0 | +| [`PATO`](https://semantic.farm/pato) | Phenotype And Trait Ontology | CC-BY-3.0 | +| [`PCO`](https://semantic.farm/pco) | Population and Community Ontology | CC0-1.0 | +| [`PO`](https://semantic.farm/po) | Plant Ontology | CC-BY-4.0 | +| [`prov`](https://semantic.farm/prov) | PROV Namespace | | +| [`qudt`](https://semantic.farm/qudt) | Quantities, Units, Dimensions, and Types Ontology | CC-BY-4.0 | +| [`RO`](https://semantic.farm/ro) | Relation Ontology | CC0-1.0 | +| [`schema`](https://semantic.farm/schema) | Schema.org | | +| [`sosa`](https://semantic.farm/sosa) | Sensor, Observation, Sample, and Actuator Ontology | [Custom](http://www.w3.org/Consortium/Legal/2015/copyright-software-and-document) | +| [`sumso`](https://semantic.farm/sumso) | Sustainable Meat Systems Ontology | CC-BY-4.0 | +| [`sweet`](https://semantic.farm/sweet) | Semantic Web for Earth and Environment Technology Ontology | CC0-1.0 | +| [`SWO`](https://semantic.farm/swo) | Software ontology | CC-BY-4.0 | +| [`taxonconcept`](https://semantic.farm/taxonconcept) | TaxonConcept Ontology | | +| [`TAXRANK`](https://semantic.farm/taxrank) | Taxonomic rank vocabulary | CC0-1.0 | +| [`tib.bk`](https://semantic.farm/tib.bk) | Basic Classification | CC0-1.0 | +| [`TO`](https://semantic.farm/to) | Plant Trait Ontology | CC-BY-4.0 | +| [`UBERON`](https://semantic.farm/uberon) | Uber Anatomy Ontology | CC-BY-3.0 | +| [`unesco.thesaurus`](https://semantic.farm/unesco.thesaurus) | UNESCO Thesaurus | CC-BY-3.0-IGO | +| [`VBO`](https://semantic.farm/vbo) | Vertebrate Breed Ontology | CC-BY-4.0 | +| [`VT`](https://semantic.farm/vt) | Vertebrate trait ontology | CC-BY-4.0 | + +## Colophon + +This page was automatically generated on 2026-05-07 using Semantic Farm +([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +by running the following commands: + +```console +$ git clone https://github.com/nfdi-de/nfdi-sections +$ cd nfdi-sections +$ uv run scripts/update_collections.py +$ git commit -am "Update WG Onto collections" +$ git push +``` diff --git a/docs/meta/wg_onto/used-ontologies/nfdi4bioimage.md b/docs/meta/wg_onto/used-ontologies/nfdi4bioimage.md index 3e0cbb6..41479b9 100644 --- a/docs/meta/wg_onto/used-ontologies/nfdi4bioimage.md +++ b/docs/meta/wg_onto/used-ontologies/nfdi4bioimage.md @@ -2,20 +2,56 @@ title: NFDI4BIOIMAGE --- -Source: `/files/meta/Used_Ontologies_at_NFDI.xlsx` (sheet: NFDI4BIOIMAGE) - -|Ontology ID|Domain|License|Modularity|Format|developed / reused / only indexed / only evaluated|Used in| -|---|---|---|---|---|---|---| -|CHEBI|Molecular entities of biological interest|CC BY 4.0||owl|reused|| -|EFO|Experimental variables|Apache license 2.0|ORDO, MONDO, CHEBI, GO, NCBITAXON, DC, NCIT, HP, FMA, OIO, OWL, UBERON, RO, PR, FBBT, OBI, OBA, IAO, SKOS, SO, BAO, DCTERMS, CLO, HANCESTRO, OGMS, PO, IDO, ZFA, RDFS, TO, CL, PATO, MPATH, DOID, FBDV, BFO, BTO, MA, MP, OMIT, UO, WBLS|owl|reused|https://idr.openmicroscopy.org/about/linked-resources.html| -|QUDT|Scientific units|CC BY 4.0|OBO_mappable|owl|reused|OME-XML| -|EDAM|Life-sciences & data management|CC BY 4.0|OBO_mappable|owl|reused|REMBI| -|BIOSCHEMA|Biology, Chemistry|CC BY 4.0|SCHEMA_aligned|rdf|reused|OME-Zarr| -|SNOMED CT|Medizin allgemein|Proprietary||rf2|reused|https://idr.openmicroscopy.org/about/linked-resources.html| -|CMPO|||||reused|| -|Ensembl|||||reused|| -|FBbi|||||reused|| -|NCBI Gene|||||reused|| -|NCBI Taxonomy|||||reused|| -|PubChem|||||reused|| -|UniProt|||||reused|| +A collection of ontologies, controlled vocabularies, database, and schemas +relevant for NFDI4BIOIMAGE + +## Maintainers + +- [Damien Goutte-Gattat](https://semantic.farm/orcid:0000-0002-6095-8718) + +Suggest a new addition to this collection +[here](https://github.com/biopragmatics/bioregistry/issues/new?template=add-collection-prefix.yml&collection=0000034&title=Add%20prefix%20X%20to%20collection%200000034). + +## Ontologies + +The following table comes from Semantic Farm collection +[`0000034`](https://semantic.farm/collection/0000034). + +| Prefix | Name | License | +| -------------------------------------------------- | ---------------------------------------- | --------------------------------------------------------------------------------------------------------------------------- | +| [`bioregistry`](https://semantic.farm/bioregistry) | Bioregistry | CC0-1.0 | +| [`CHEBI`](https://semantic.farm/chebi) | Chemical Entities of Biological Interest | CC-BY-4.0 | +| [`CL`](https://semantic.farm/cl) | Cell Ontology | CC-BY-4.0 | +| [`CLO`](https://semantic.farm/clo) | Cell Line Ontology | CC-BY-3.0 | +| [`cmpo`](https://semantic.farm/cmpo) | Cellular Microscopy Phenotype Ontology | | +| [`dicom`](https://semantic.farm/dicom) | Healthcare metadata - DICOM ontology | | +| [`DOID`](https://semantic.farm/doid) | Human Disease Ontology | CC0-1.0 | +| [`edam`](https://semantic.farm/edam) | EDAM Ontology | CC-BY-SA-4.0 | +| [`EFO`](https://semantic.farm/efo) | Experimental Factor Ontology | Apache-2.0 | +| [`FBbi`](https://semantic.farm/fbbi) | Biological Imaging Methods Ontology | CC-BY-4.0 | +| [`GO`](https://semantic.farm/go) | Gene Ontology | CC-BY-4.0 | +| [`mesh`](https://semantic.farm/mesh) | Medical Subject Headings | CC0-1.0 | +| [`MONDO`](https://semantic.farm/mondo) | Mondo Disease Ontology | CC-BY-4.0 | +| [`MP`](https://semantic.farm/mp) | Mammalian Phenotype Ontology | CC-BY-4.0 | +| [`MPATH`](https://semantic.farm/mpath) | Mouse pathology ontology | CC-BY-3.0 | +| [`NCBITaxon`](https://semantic.farm/ncbitaxon) | NCBI Taxonomy | CC0-1.0 | +| [`OBI`](https://semantic.farm/obi) | Ontology for Biomedical Investigations | CC-BY-4.0 | +| [`radlex`](https://semantic.farm/radlex) | RSNA Informatics RadLex | [Custom](http://www.rsna.org/uploadedFiles/RSNA/Content/Informatics/RadLex_License_Agreement_and_Terms_of_Use_V2_Final.pdf) | +| [`snomedct`](https://semantic.farm/snomedct) | SNOMED CT (International Edition) | [Custom](https://uts.nlm.nih.gov/uts/assets/LicenseAgreement.pdf) | +| [`SWO`](https://semantic.farm/swo) | Software ontology | CC-BY-4.0 | +| [`UBERON`](https://semantic.farm/uberon) | Uber Anatomy Ontology | CC-BY-3.0 | +| [`UO`](https://semantic.farm/uo) | Units of measurement ontology | CC-BY-3.0 | + +## Colophon + +This page was automatically generated on 2026-05-07 using Semantic Farm +([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +by running the following commands: + +```console +$ git clone https://github.com/nfdi-de/nfdi-sections +$ cd nfdi-sections +$ uv run scripts/update_collections.py +$ git commit -am "Update WG Onto collections" +$ git push +``` diff --git a/docs/meta/wg_onto/used-ontologies/nfdi4cat.md b/docs/meta/wg_onto/used-ontologies/nfdi4cat.md deleted file mode 100644 index 7bc04a6..0000000 --- a/docs/meta/wg_onto/used-ontologies/nfdi4cat.md +++ /dev/null @@ -1,28 +0,0 @@ ---- -title: NFDI4Cat ---- - -Source: `/files/meta/Used_Ontologies_at_NFDI.xlsx` (sheet: NFDI4Cat) - -|Ontology ID|Domain|License|Modularity|Format|developed / reused / only indexed / only evaluated|Used in| -|---|---|---|---|---|---|---| -|EMMO|TLO - Material Modelling Orientated|CC BY 4.0|own top-level & diverse sub Onto's|owl|reused|| -|AFO|Chemistry and Analytics|CC BY 4.0|BFO 2020, contains many sub-ontologies like: AFR,|owl|reused|Alotrop Foundation / ADF| -|CHMO|Chemistry and Laboratory Practices|CC BY 4.0|BFO & OBO based|owl|reused|| -|CHEMINF|Chemistry - Photochemistry|CC0 1.0|BFO & OBO based|owl|reused|| -|VIMMP ontologies|Process and Material Modelling|GNU LGPL v3|these are several ontologies|owl|only evaluated|Marketplace Initiative| -|BFO|Upper level (classes only)|CC BY 4.0|OBO backbone|owl|reused|¿300 ontologies & ¿50 organizations, PubChem| -|ChEBI|Chemistry - chemical entities|CC BY 4.0|BFO & OBO based|owl|reused|| -|RXNO|Chemistry - synthetic reactions|CC BY 4.0|BFO & OBO based|owl|reused|| -|BAO|Biochemistry - Experiments|CC BY 4.0|OBO_mappable|owl|reused|| -|CAO|Chemistry - analytics|CC BY 3.0|OBO_mappable|owl|reused|| -|CIF|Chemistry - crystallography|CC BY 4.0|EMMO|owl|only evaluated|| -|EDAM|Life-sciences & data management|GNU LGPL v3.0|OBO_mappable|owl|only evaluated|| -|M4I|mid-level ontology|CC BY 4.0|partially aligned with: BFO, PROV, DCAT, FOAF and SCHEMA|owl|reused|| -|MOP|Chemistry - molecular reactions|CC BY 4.0|BFO & OBO based|owl|only evaluated|| -|MS|Chemistry - mass spectrometry|CC BY 4.0|OBO_mappable|owl|only evaluated|| -|OBI|Biomedical|CC BY 4.0|BFO & OBO based|owl|reused|| -|OM|Scientific units|CC BY 4.0|no mapping/alignment to others known|owl|reused|| -|OntoCAPE|Upper level & engineering|GNU GPLv2|no mapping/alignment to others known|owl|only indexed|| -|REX|Chemistry - physico-chemical processes||mapped to in other ontologies (e.g. CHMO)|owl|reused|| -|SBO|BioChemistry|Artistic-2.0 license|BFO & OBO based|owl|reused|| diff --git a/docs/meta/wg_onto/used-ontologies/nfdi4chem.md b/docs/meta/wg_onto/used-ontologies/nfdi4chem.md index 80b5d59..4b2f084 100644 --- a/docs/meta/wg_onto/used-ontologies/nfdi4chem.md +++ b/docs/meta/wg_onto/used-ontologies/nfdi4chem.md @@ -2,56 +2,92 @@ title: NFDI4Chem --- -The review [The current landscape of author guidelines in chemistry through the lens of research data sharing](https://doi.org/10.1515/pac-2022-1001) provides an overview and usage guidance for ontologies in chemistry. - -The table below is from the WG Ontology collection spreadsheet. - -Source: `/files/meta/Used_Ontologies_at_NFDI.xlsx` (sheet: NFDI4Chem) - -|Ontology ID|Domain|License|Modularity|Format|Used in|Comments|developed / reused / only indexed / only evaluated|NFDI4Chem contributions| -|---|---|---|---|---|---|---|---|---| -|AFO|Chemistry - all chemical domains|CC BY 4.0|BFO 2020, questionable OBO alignment, imports: DCTERMS, CARO, SKOS, DC, OWL, RDFS, NCIT, OBI, NCBITAXON, IAO, PATO, ENVO, BFO, RO, CHEBI, CHMO|owl|Allotrope™||reused|| -|ChEBI|Chemistry - chemical entities|CC BY 4.0|OBO_based, BFO_mappable, imports: RO, IAO, RDFS, OWL, OIO|owl|YMDB, HMDB, PubChem, MassBank, KNApSAcK, UM-BBD, GMD, SMID-DB||reused|| -|ChemOnt|Chemistry - chemical entities|Custom OA license|BFO_mappable, ChEBI_mappable, OBO_mappable|owl|YMDB, HMDB, T3DB, ECMDB, DrugBank, PubChem, ChEBI, LIPID MAPS, MoNA||only evaluated|| -|CHMO|Chemistry - chemical methods|CC BY 4.0|OBO_based, extends OBI, maps_to: "FIX, REX", imports: CHEBI, OIO, DC, IAO, DCTERMS, OBI, MS, RDFS, BFO, OWL, RO, OBCS|owl|Chemotion, Allotrope™||reused|on GitHub| -|CHEMINF|Chemistry - cheminformatics|CC0 1.0|OBO_based, extends IAO, imports: OIO, DC, OBI, RDFS, OWL, IAO, PR, DCTERMS, OMO, PATO, BFO, RO, CHEBI, APOLLO_SV, GO, UO, SKOS|owl|PubChem, Open PHACTS||reused|on GitHub| -|MS|Chemistry - mass spectrometry|CC BY 4.0|OBO_mappable, imports: CARO, CHEBI, RO, GO, NCBITAXON, DC, NCIT, PATO, UBERON, OBI, RDFS, OIO, DCTERMS, PR, IAO, SKOS, SO, NBO, OWL, OGMS, PCO, CL, ENVO, BFO, UO, BSPO, STATO|owl|mzML||reused|| -|MOP|Chemistry - molecular reactions|CC BY 4.0|BFO aligned, OBO based, imports: CHEBI, OIO, DC, IAO, DCTERMS, RDFS, BFO, RXNO, RO|owl|RXNO||reused|on GitHub| -|nmrCV|Chemistry - NMR spectroscopy|Public Domain Mark 1.0|BFO aligned, OBO_mappable, imports: DC, RDFS, OIO, DCTERMS, SKOS, IAO, BFO|owl|MetaboLights, HMDB||reused|on GitHub| -|FIX|Chemistry - physico-chemical methods and properties|unkown|orphaned, use discouraged|owl||OUTDATED/ORPHANED; not encurraged for reuse|only indexed|| -|REX|Chemistry - physico-chemical processes|unkown|orphaned, use discouraged|owl||OUTDATED/ORPHANED; not encurraged for reuse|only indexed|| -|BFO|Upper level (classes only)|CC BY 4.0|BFO version 2.0 classes only, OBO backbone|owl|~300 ontologies & ~50 organizations, PubChem||reused|| -|IAO|Information artifacts|CC BY 4.0|BFO aligned, OBO based, imports: DC, OBI, RDFS, DCTERMS, OMO, OIO, PATO, BFO, RO, APOLLO_SV, UO|owl|OBO Foundry, Allotrope™, PubChem, ISA tools||reused|on GitHub| -|OBI|Biomedicine|CC BY 4.0|BFO aligned, OBO based, imports: CHEBI, GO, DC, NCBITAXON, OWL, OMRSE, UBERON, VO, RDFS, IAO, SO, PR, DCTERMS, CLO, OGMS, HP, IDO, OPL, OBA, PATO, CL, OIO, BFO, RO, COB, APOLLO_SV, ENVO, UO, CHMO|owl|OBO Foundry, Allotrope™, PubChem||reused|on GitHub| -|UO|Scientific units|CC BY 3.0|OBO_based|owl|OBO Foundry, UOM, PubChem||reused|on GitHub| -|OM|Scientific units|CC BY 4.0|no mapping/alignment to others known|owl|alignment probably not needed for use case of reusing for units||reused|| -|QUDT|Scientific units|CC BY 4.0|OBO_mappable|owl|Open PHACTS||reused|| -|PATO|Phenotypic & physical qualities|CC BY 3.0|OBO_based|owl|OBO Foundry, Allotrope™||reused|on GitHub| -|SEPIO|Scientific Evidence and Provenance|CC BY 3.0|BFO aligned, OBO based (imports from OBI, RO, IAO, COB, PATO, STATO), partial PROV-O alignement (e.g. Agent & Activity)|owl|Ga4GH Variant Annotation Model||reused|| -|ENVO|environments,environmental processes, ecosystems, habitats, and related entities|CC0 1.0|OBO_based, BFO_aligned|owl|||reused|| -|PROV-O|general scientific and provenance|W3C License|W3C_based|owl|||reused|| -|SWO|software domain|CC BY 4.0|BFO aligned|owl|||reused|| -|SIO|Upper level|CC BY 4.0|BFO aligned|owl|PubChem, Bio2RDF, SADI Semantic Web Services, DisGeNET’s gene-disease associations, EBI’s Gene Expression Atlas, Graph4Code||reused|| -|EDAM|Life-sciences & data management|CC BY 4.0|OBO_mappable|owl|EMBOSS, Bio-jETI||reused|| -|EFO|experimental variables|Apache License 2.0|BFO aligned|owl|EBI databases, core ontology for OpenTargets.org, NHGRI GWAS catalogue||reused|on GitHub| -|RO|General science w/focus on life sciences|CC0 1.0|OBO_based, BFO_aligned, DC, OIO, DCTERMS, IAO, SKOS, OBI, OGMS, OMO, UBERON, RDFS, PATO, ENVO, BFO, GO, CL, CHEBI|owl|all OBO ontologies and many others||reused|on GitHub| -|DUO|data use conditions|CC BY 4.0|OBO_based, BFO_aligned|owl|||reused|| -|TIME|Time|CC BY 4.0|no mapping/alignment to others known, W3C_based|owl|||reused|| -|PROCO|Chemistry - process chemistry|CC BY 4.0|AFO & OBO based, BFO_aligned|owl|Allotrope™||reused|| -|SOSA|general scientific domain (Sensor, Observation, Sample, and Actuator)|W3C License|W3C_based (imports FOAF & TIME)|owl|||only indexed|| -|SSN|general scientific domain (Sensor, Observation, Sample, and Actuator)|W3C License|W3C_based (imports SOSA, FOAF & TIME)|owl|||only indexed|| -|SSN-SYSTEM|SSN extention|W3C License|W3C_based|owl|||only indexed|| -|OBOE|general scientific domain (scientific observation and measurement)|CC BY 3.0||owl|||only indexed|| -|BTO|Biology - enzyme comprising tissues, cell lines, cell types and cell cultures|CC BY 4.0|no mapping/alignment to others known, slim ontological commitment allows for broad modular reuse|owl||OBO ontology; indexed in NFDI4Chem due to NMRxiv's need for annotating biosogicalsamples|only indexed|| -|OntoKin|Chemistry - reaction kinetics|Unknown|based on OntoCAPE upper level & modules, OBO_incompatible|owl|J-Park Simulator||only indexed|| -|CHIRO|Chemistry - roles of chemical entities|CC0 1.0|OBO_based, extends ChEBI's role branch, BFO_aligned|owl|Unknown||reused|| -|MI|Biology - structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions|CC BY 4.0|no mapping/alignment to others known|owl||unsure why indexed|only indexed|| -|NCIT|Biology - reference terminology that includes broad coverage of the cancer domain, including cancer related diseases, findings and abnormalities|CC BY 4.0|OBO_based|owl||unsure why indexed, not BFO aligned but OBO Edition|only indexed|| -|MOD|Biology - protein chemical modifications|CC BY 4.0|no mapping/alignment to others known|owl||unsure why indexed|only indexed|| -|REPRODUCEME|General science|CC BY-NC-SA 2.0|P-PLAN & PROV-O extention|owl|||only indexed|| -|OntoCAPE|Upper level & engineering|GNU GPLv2|no mapping/alignment to others known|owl|J-Park Simulator||only evaluated|| -|RXNO|Chemistry - synthetic reactions|CC BY 4.0|OBO_based, extends MOP & OBI, BFO_aligned|owl|NameRXN, Wikipedia, Chemotion||reused|on GitHub| -|VIBSO|Chemistry - vibrational spectroscopy|CC BY 4.0|OBO_based, extends CHMO & OBI, BFO_aligned|owl|NFDI4Chem||developed|on GitHub| -|DCTERMS|General|CC BY 4.0|used as module for annotation properties|rdf||used for ontology annotations, e.g contributor, license etc.|reused|| -|DCAT|General|W3C License|W3C_based|owl|NFDI4Chem Search service||reused| -|BIOSCHEMA|Biology, Chemistry|CC BY 4.0|SCHEMA_aligned|rdf|NFDI4Chem Search service, and possibly others||reused|yes by TA2 & TA4| +A collection of ontologies relevant within the +[NFDI4Chem project](https://www.nfdi4chem.de/) that is mostly based on the +overview paper +[Ontologies4Chem: the landscape of ontologies in chemistry](https://doi.org/10.1515/pac-2021-2007). + +NFDI4Chem deploys a [custom instance](https://terminology.nfdi4chem.de/ts/) of +the Ontology Lookup Service (OLS), called NFDI4Chem Terminology Services (TS), +that provides the ontologies in this list. This list contains ontologies that +cover various domains of chemistry (e.g. ChEBI, CHMO, and RXNO), those that are +dependencies of these chemistry specific ontologies (e.g. BFO, RO, IAO, and OBI) +as well as those ontologies, which where indexed in the NFDI4Chem TS for +interoperability research purposes (e.g. PROV-O, SOSA, and OBOE). + +## Maintainers + +- [Philip Strömert](https://semantic.farm/orcid:0000-0002-1595-3213) + +Suggest a new addition to this collection +[here](https://github.com/biopragmatics/bioregistry/issues/new?template=add-collection-prefix.yml&collection=0000014&title=Add%20prefix%20X%20to%20collection%200000014). + +## Ontologies + +The following table comes from Semantic Farm collection +[`0000014`](https://semantic.farm/collection/0000014), which is automatically +synced from the TIB Terminology Service collection +[`nfdi4chem`](https://service.tib.eu/terminology/collections/nfdi4chem). + +| Prefix | Name | License | Comment | +| -------------------------------------------------------------------- | ------------------------------------------------------------------------------------ | --------------------------------------------------------------------------------- | --------------------------------------------------------------------- | +| [`afo`](https://semantic.farm/afo) | Allotrope Merged Ontology Suite | [Custom](http://purl.allotrope.org/voc/copyright) | | +| [`BFO`](https://semantic.farm/bfo) | Basic Formal Ontology | CC-BY-4.0 | | +| [`BTO`](https://semantic.farm/bto) | BRENDA Tissue Ontology | CC-BY-4.0 | | +| [`CHEBI`](https://semantic.farm/chebi) | Chemical Entities of Biological Interest | CC-BY-4.0 | Used in YMDB, HMDB, PubChem, MassBank, KNApSAcK, UM-BBD, GMD, SMID-DB | +| [`CHEMINF`](https://semantic.farm/cheminf) | Chemical Information Ontology | CC0-1.0 | | +| [`ChEMROF`](https://semantic.farm/chemrof) | Chemical Entity Materials and Reactions Ontological Framework | CC0-1.0 | | +| [`CHIRO`](https://semantic.farm/chiro) | ChEBI Integrated Role Ontology | CC0-1.0 | | +| [`CHMO`](https://semantic.farm/chmo) | Chemical Methods Ontology | CC-BY-4.0 | | +| [`DUO`](https://semantic.farm/duo) | Data Use Ontology | CC-BY-4.0 | | +| [`edam`](https://semantic.farm/edam) | EDAM Ontology | CC-BY-SA-4.0 | | +| [`EFO`](https://semantic.farm/efo) | Experimental Factor Ontology | Apache-2.0 | | +| [`enm`](https://semantic.farm/enm) | eNanoMapper ontology | CC-BY-3.0 | | +| [`ENVO`](https://semantic.farm/envo) | Environment Ontology | CC0-1.0 | | +| [`fair`](https://semantic.farm/fair) | FAIR Vocabulary | | | +| [`FIX`](https://semantic.farm/fix) | Physico-chemical methods and properties | | | +| [`gainesville.core`](https://semantic.farm/gainesville.core) | Gainesville Core Ontology | CC-BY-3.0 | | +| [`IAO`](https://semantic.farm/iao) | Information Artifact Ontology | CC-BY-4.0 | | +| [`MOD`](https://semantic.farm/mod) | Protein modification | CC-BY-4.0 | | +| [`MOP`](https://semantic.farm/mop) | Molecular Process Ontology | CC-BY-4.0 | | +| [`MS`](https://semantic.farm/ms) | Mass spectrometry ontology | CC-BY-3.0 | | +| [`NCIT`](https://semantic.farm/ncit) | NCI Thesaurus | CC-BY-4.0 | | +| [`NMR`](https://semantic.farm/nmr) | NMR-instrument specific component of metabolomics investigations | | | +| [`OBI`](https://semantic.farm/obi) | Ontology for Biomedical Investigations | CC-BY-4.0 | | +| [`oboe`](https://semantic.farm/oboe) | The Extensible Observation Ontology | CC-BY-3.0 | | +| [`om`](https://semantic.farm/om) | Ontology of units of Measure | CC-BY-4.0 | | +| [`ontorxn`](https://semantic.farm/ontorxn) | OntoRXN | CC-BY-4.0 | | +| [`PATO`](https://semantic.farm/pato) | Phenotype And Trait Ontology | CC-BY-3.0 | | +| [`PROCO`](https://semantic.farm/proco) | Process Chemistry Ontology | CC-BY-4.0 | | +| [`prov`](https://semantic.farm/prov) | PROV Namespace | | | +| [`reproduceme`](https://semantic.farm/reproduceme) | REPRODUCE-ME Ontology | | | +| [`REX`](https://semantic.farm/rex) | Physico-chemical process | | | +| [`RO`](https://semantic.farm/ro) | Relation Ontology | CC0-1.0 | | +| [`RXNO`](https://semantic.farm/rxno) | Name Reaction Ontology | CC-BY-4.0 | | +| [`SEPIO`](https://semantic.farm/sepio) | Scientific Evidence and Provenance Information Ontology | CC-BY-3.0 | | +| [`SIO`](https://semantic.farm/sio) | Semanticscience Integrated Ontology | CC-BY-4.0 | | +| [`sosa`](https://semantic.farm/sosa) | Sensor, Observation, Sample, and Actuator Ontology | [Custom](http://www.w3.org/Consortium/Legal/2015/copyright-software-and-document) | | +| [`ssn`](https://semantic.farm/ssn) | Semantic Sensor Network Ontology | [Custom](http://www.w3.org/Consortium/Legal/2015/copyright-software-and-document) | | +| [`ssn.system`](https://semantic.farm/ssn.system) | System capabilities, operating ranges, and survival ranges ontology | [Custom](http://www.w3.org/Consortium/Legal/2015/copyright-software-and-document) | | +| [`SWO`](https://semantic.farm/swo) | Software ontology | CC-BY-4.0 | | +| [`time`](https://semantic.farm/time) | Time Ontology in OWL | CC-BY-4.0 | | +| [`UO`](https://semantic.farm/uo) | Units of measurement ontology | CC-BY-3.0 | | +| [`vibso`](https://semantic.farm/vibso) | Vibrational Spectroscopy Ontology | CC-BY-4.0 | | +| [`voc4cat`](https://semantic.farm/voc4cat) | A vocabulary for the catalysis disciplines | CC0-1.0 | | +| [`worldavatar.compchem`](https://semantic.farm/worldavatar.compchem) | Computational Chemistry Ontology | | | +| [`worldavatar.kin`](https://semantic.farm/worldavatar.kin) | Ontology for Chemical Kinetic Reaction Mechanisms | | | +| [`worldavatar.os`](https://semantic.farm/worldavatar.os) | OntoSpecies - Chemical Species Ontology for Data Integration and Knowledge Discovery | | | + +## Colophon + +This page was automatically generated on 2026-05-07 using Semantic Farm +([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +by running the following commands: + +```console +$ git clone https://github.com/nfdi-de/nfdi-sections +$ cd nfdi-sections +$ uv run scripts/update_collections.py +$ git commit -am "Update WG Onto collections" +$ git push +``` diff --git a/docs/meta/wg_onto/used-ontologies/nfdi4culture.md b/docs/meta/wg_onto/used-ontologies/nfdi4culture.md index f59546f..49cd458 100644 --- a/docs/meta/wg_onto/used-ontologies/nfdi4culture.md +++ b/docs/meta/wg_onto/used-ontologies/nfdi4culture.md @@ -2,37 +2,71 @@ title: NFDI4Culture --- -Source: `/files/meta/Used_Ontologies_at_NFDI.xlsx` (sheet: NFDI4Culture) - -|BARTOC URI|Ontology ID|Domain|License|Modularity|Format|developed / reused / only indexed / only evaluated|Used in|Comments|NFDI4Culture contributions| -|---|---|---|---|---|---|---|---|---|---| -||NFDICO|Culture||imports SCHEMA, maps_to: "DCAT, DOAP, FOAF, FABIO, SD, VCARD, VIVO, SWO, WIKIDATA, ORG, FRAPO, MODSCI, DBO, SCHEMA, DCTERMS, IAO, OBI"|owl|developed|NFDI-MatWerk, NFDI4DataScience, NFDI4Memory||| -||Culture Graph Interchange Format (CGIF)|Culture|CC BY 4.0|imports SCHEMA, maps_to: "DCAT, DOAP, FOAF, FABIO, SD, VCARD, VIVO, SWO, WIKIDATA, ORG, FRAPO, MODSCI, DBO, SCHEMA, DCTERMS, IAO, OBI"|rdf|developed|||| -|http://bartoc.org/en/node/20291|CIDOC-CRM|Culture|CC BY 4.0||owl|reused|||| -|http://bartoc.org/en/node/20291|Erlangen CRM|Culture|CC BY-SA 3.0|based on CIDOC-CRM|owl|only indexed|||| -||LIDO|Culture|CC BY 4.0|based on CIDOC-CRM, CDWA, museumdat, and SPECTRUM|xsd|reused|||| -|http://bartoc.org/en/node/18250|SCHEMA|general|CC BY-SA 3.0||rdf|reused|||| -|http://bartoc.org/en/node/18274|SKOS|general|W3C License||rdf|only indexed||meta model/terminology framework|| -|http://bartoc.org/en/node/459|Iconclass|Culture: Art History|||skos|reused|||| -||GEONAMES|General: Geographic Names|CC BY 4.0||owl|reused||The ontology describes the classes in which the countries and other locations are encoded as RDF in the GeoNames database. So if the RDF URIs for the named individuals contained therin are reused, one reuses indirectly the ontology.|| -||DCAT||CC BY 4.0||owl|reused|NFDICO||| -||DOAP||Apache License 2.0|imports FOAF|owl|reused|NFDICO|https://github.com/ewilderj/doap|| -||FOAF||||owl|reused|NFDICO||| -||FABIO||CC BY 4.0|imports FRBR, DCTERMS, PRISM|owl|reused|NFDICO||| -||SD||CC BY 2.0|extends: SCHEMA, CODEMETA (maps to WIKIDATA)|owl|reused|NFDICO||| -||VCARD||||owl|reused|NFDICO||| -||VIVO||CC0 1.0||owl|reused|NFDICO||| -||SWO||||owl|reused|NFDICO||| -||WIKIDATA||||owl|reused|NFDICO||| -||ORG||W3C License||owl|reused|NFDICO||| -||FRAPO||CC BY 4.0|imports FOAF|owl|reused|NFDICO||| -||MODSCI||CC BY 4.0|imports: SKOS, FOAF, SWEET|owl|reused|NFDICO||| -||DBO||CC BY-SA 3.0|DBO - TBox with DBPEDIA (ABox) as part, mapped to SCHEMA, WIKIDATA|owl|reused|NFDICO||| -||SCHEMA||||owl|reused|NFDICO||| -||DCTERMS||||owl|reused|NFDICO||| -||IAO||||owl|reused|NFDICO||| -||OBI||||owl|reused|NFDICO||| -|http://bartoc.org/en/node/430|GND|general|CC0 1.0||rdf|reused|||| -|http://bartoc.org/en/node/2053|VIAF|general|CC BY 1.0||rdf|reused|||| -|http://bartoc.org/en/node/1940|WIKIDATA|general|CC0 1.0||rdf|reused|||| -||BFO2020|general|||||||| +A placeholder collection of ontologies, controlled vocabularies, and schemas +relevant for the NFDI4Culture Consortium seeded from corresponding the +[TIB OLS collection](https://service.tib.eu/terminology/collections/nfdi4culture). +The +[NFDI Section Metadata WG Ontology Harmonization and Mapping](https://github.com/nfdi-de/section-metadata-wg-onto/) +is in the process of identifying NFDI4Culture Consortium members appropriate for +maintaining this collection. + +## Maintainers + +- [Tabea Tietz](https://semantic.farm/orcid:0000-0002-1648-1684) + +Suggest a new addition to this collection +[here](https://github.com/biopragmatics/bioregistry/issues/new?template=add-collection-prefix.yml&collection=0000025&title=Add%20prefix%20X%20to%20collection%200000025). + +## Ontologies + +The following table comes from Semantic Farm collection +[`0000025`](https://semantic.farm/collection/0000025), which is automatically +synced from the TIB Terminology Service collection +[`nfdi4culture`](https://service.tib.eu/terminology/collections/nfdi4culture). + +| Prefix | Name | License | +| ------------------------------------------------------------ | ----------------------------------------------------------------------------------- | ---------- | +| [`BFO`](https://semantic.farm/bfo) | Basic Formal Ontology | CC-BY-4.0 | +| [`bot`](https://semantic.farm/bot) | Building Topology Ontology | | +| [`cidoc.crm`](https://semantic.farm/cidoc.crm) | CIDOC Conceptual Reference Model | | +| [`dbo`](https://semantic.farm/dbo) | DBPedia Ontology | | +| [`dcat`](https://semantic.farm/dcat) | Data Catalog | CC-BY-4.0 | +| [`dcterms`](https://semantic.farm/dcterms) | Dublin Core Metadata Initiative Terms | | +| [`doap`](https://semantic.farm/doap) | Description of a Project | | +| [`fabio`](https://semantic.farm/fabio) | FaBiO, the FRBR-aligned Bibliographic Ontology | CC-BY-4.0 | +| [`foaf`](https://semantic.farm/foaf) | Friend of a Friend | CC-BY-1.0 | +| [`FRAPO`](https://semantic.farm/frapo) | Funding, Research Administration and Projects Ontology | | +| [`geonames`](https://semantic.farm/geonames) | GeoNames | CC-BY-4.0 | +| [`gesah`](https://semantic.farm/gesah) | GESAH Graphic Arts Ontology | | +| [`gnd`](https://semantic.farm/gnd) | Gemeinsame Normdatei | CC0-1.0 | +| [`IAO`](https://semantic.farm/iao) | Information Artifact Ontology | CC-BY-4.0 | +| [`iconclass`](https://semantic.farm/iconclass) | Iconclass Classification | ODbL-1.0 | +| [`lido`](https://semantic.farm/lido) | Lightweight Information Describing Objects | CC-BY-4.0 | +| [`modsci`](https://semantic.farm/modsci) | Modern Science Ontology | | +| [`nfdi4culture.cto`](https://semantic.farm/nfdi4culture.cto) | NFDI4Culture Ontology | CC0-1.0 | +| [`OBI`](https://semantic.farm/obi) | Ontology for Biomedical Investigations | CC-BY-4.0 | +| [`ohdab`](https://semantic.farm/ohdab) | Ontology of the historical German-language nomenclature for offices and professions | | +| [`okn.sd`](https://semantic.farm/okn.sd) | The Software Description Ontology | | +| [`org`](https://semantic.farm/org) | Core organization ontology | | +| [`premis`](https://semantic.farm/premis) | PREMIS 3 Ontology | | +| [`schema`](https://semantic.farm/schema) | Schema.org | | +| [`skos`](https://semantic.farm/skos) | Simple Knowledge Organization System | | +| [`SWO`](https://semantic.farm/swo) | Software ontology | CC-BY-4.0 | +| [`vcard`](https://semantic.farm/vcard) | Virtual Contact File | | +| [`viaf`](https://semantic.farm/viaf) | Virtual International Authority File | ODC-By-1.0 | +| [`vivo`](https://semantic.farm/vivo) | VIVO Ontology | Unlicense | +| [`wikidata`](https://semantic.farm/wikidata) | Wikidata | CC0-1.0 | + +## Colophon + +This page was automatically generated on 2026-05-07 using Semantic Farm +([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +by running the following commands: + +```console +$ git clone https://github.com/nfdi-de/nfdi-sections +$ cd nfdi-sections +$ uv run scripts/update_collections.py +$ git commit -am "Update WG Onto collections" +$ git push +``` diff --git a/docs/meta/wg_onto/used-ontologies/nfdi4datascience.md b/docs/meta/wg_onto/used-ontologies/nfdi4datascience.md index 91de699..6a929da 100644 --- a/docs/meta/wg_onto/used-ontologies/nfdi4datascience.md +++ b/docs/meta/wg_onto/used-ontologies/nfdi4datascience.md @@ -2,9 +2,40 @@ title: NFDI4DataScience --- -Source: `/files/meta/Used_Ontologies_at_NFDI.xlsx` (sheet: NFDI4DataScience) +A placeholder collection of ontologies, controlled vocabularies, and schemas +relevant for the NFDI4DataScience Consortium created by the +[NFDI Section Metadata WG Ontology Harmonization and Mapping](https://github.com/nfdi-de/section-metadata-wg-onto/). +The working group is in the process of identifying NFDI4DataScience Consortium +members appropriate for maintaining this collection. -|Ontology ID|Domain|License|Modularity|Format|developed / reused / only indexed / only evaluated|Used in| -|---|---|---|---|---|---|---| -|SCHEMA|General|CC BY-SA 3.0||rdf|reused|Portal (under construction)| -|NFDICO|Research information for NFDI Consortia|CC BY 4.0|imports SCHEMA, maps_to: "DCAT, DOAP, FOAF, FABIO, SD, VCARD, VIVO, SWO, WIKIDATA, ORG, FRAPO, MODSCI, DBO, SCHEMA, DCTERMS, IAO, OBI"|owl|reused|NFDI4CUlture, NFDI-MatWerk, NFDI4Memory| +## Maintainers + +- [Benjamin Zapilko](https://semantic.farm/orcid:0000-0001-9495-040X) + +Suggest a new addition to this collection +[here](https://github.com/biopragmatics/bioregistry/issues/new?template=add-collection-prefix.yml&collection=0000029&title=Add%20prefix%20X%20to%20collection%200000029). + +## Ontologies + +The following table comes from Semantic Farm collection +[`0000029`](https://semantic.farm/collection/0000029). + +| Prefix | Name | License | +| ---------------------------------------------- | ------------------------- | ------- | +| [`nfdi.core`](https://semantic.farm/nfdi.core) | NFDI Core Ontology | CC0-1.0 | +| [`nfdi4dso`](https://semantic.farm/nfdi4dso) | NFDI4DataScience Ontology | | +| [`schema`](https://semantic.farm/schema) | Schema.org | | + +## Colophon + +This page was automatically generated on 2026-05-07 using Semantic Farm +([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +by running the following commands: + +```console +$ git clone https://github.com/nfdi-de/nfdi-sections +$ cd nfdi-sections +$ uv run scripts/update_collections.py +$ git commit -am "Update WG Onto collections" +$ git push +``` diff --git a/docs/meta/wg_onto/used-ontologies/nfdi4earth.md b/docs/meta/wg_onto/used-ontologies/nfdi4earth.md index 3b99ac2..358ae92 100644 --- a/docs/meta/wg_onto/used-ontologies/nfdi4earth.md +++ b/docs/meta/wg_onto/used-ontologies/nfdi4earth.md @@ -2,35 +2,64 @@ title: NFDI4Earth --- -Source: `/files/meta/Used_Ontologies_at_NFDI.xlsx` (sheet: NFDI4Earth) - -|Ontology ID|Ontology|Domain|License|Format uncontrolled|Format|developed / reused / only indexed / only evaluated|Modularity|Obofoundry|OLS URL|Bioportal|Github|File URL|Other URL|Description| |Useful Links:|OBO Foundry|NCBO BioPortal|OLS ontology search|GFBio Terminology Service| -|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---| -|BCO|Biological Collections Ontology|biology|CC0 1.0|OWL|owl|reused|BFO|https://ontobee.org/ontology/BCO|https://www.ebi.ac.uk/ols/ontologies/bco|https://bioportal.bioontology.org/ontologies/BCO|https://github.com/BiodiversityOntologies/bco|https://bioportal.bioontology.org/ontologies/BCO||OBO: The Biological Collections Ontology (BCO) is a being developed as an application ontology as part of the Biocode Commons project, within the OBO Foundry framework. The goal of the BCO is to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys.<br/><br/>GFBio: The biological collection ontology includes consideration of the distinctions between individuals, organisms, voucher specimens, lots, and samples the relations between these entities, and processes governing the creation and use of "samples". Within scope as well are properties including collector, location, time, storage environment, containers, institution, and collection identifiers.||Comments:|Please (also) check out the DataPlant sheet, there is some overlap ... Gruss, Steffen|||| -|ChEBI|Chemical Entities of Biological Interest Ontology|chemistry|CC BY 4.0|OWL|owl|reused|OBO|https://obofoundry.org/ontology/chebi.html|https://www.ebi.ac.uk/ols/ontologies/chebi|https://bioportal.bioontology.org/ontologies/CHEBI|https://github.com/ebi-chebi/ChEBI|https://bioportal.bioontology.org/ontologies/CHEBI|http://www.ebi.ac.uk/chebi|GitHub: Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds. The term ‘molecular entity’ refers to any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity.<br/><br/>Other source: A structured classification of chemical compounds of biological relevance.| -|ENVO|Environment Ontology|environmental|CC0 1.0|OWL|owl|reused|BFO|https://obofoundry.org/ontology/envo.html|https://www.ebi.ac.uk/ols/ontologies/envo|https://bioportal.bioontology.org/ontologies/ENVO|https://github.com/EnvironmentOntology/envo|https://raw.githubusercontent.com/EnvironmentOntology/envo/master/envo.owl|http://environmentontology.org/|BioPortal: The most up-to-date information about ENVO is available here: http://www.obofoundry.org/ontology/envo.html EnvO is an OBO Foundry and Library ontology for the concise, controlled description of environmental entities such as ecosystems, environmental processes, and environmental qualities. It closely interoperates with a broad collection of other OBO ontologies and is used in a diverse range of projects.| -|FLOPO|Flora Phenotype Ontology|anatomical|CC BY 3.0|OWL|owl|reused|OBO|https://obofoundry.org/ontology/flopo.html|https://www.ebi.ac.uk/ols/ontologies/flopo|https://bioportal.bioontology.org/ontologies/FLOPO|https://github.com/flora-phenotype-ontology/flopoontology|https://github.com/flora-phenotype-ontology/flopoontology/tree/master/ontology||BioPortal: The Flora Phenotype Ontology is an ontology of phenotypes reported in Floras. The original version was developed at the pro-iBiosphere Hackathon in Leiden. This is the pre-classified version of the ontology; the original OWL file is at https://github.com/flora-phenotype-ontology/flopoontology/blob/master/ontology/flopo.owl The Flora Phenotype Ontology is generated from the Flora Malesiana, Flora Gabon, Flora of Central Africa, and a collection of Kew's African Floras. Every class in the ontology has at least one taxon annotation. The (draft) taxon annotation are available at http://jagannath.pdn.cam.ac.uk/plant/flora/clean-rerun/| -|NCBITAXON|National Center for Biotechnology Information Organismal Classification|biology|CC0 1.0|OWL|owl|reused|OBO|https://obofoundry.org/ontology/ncbitaxon.html|https://www.ebi.ac.uk/ols/ontologies/ncbitaxon|https://bioportal.bioontology.org/ontologies/NCBITAXON|https://github.com/obophenotype/ncbitaxon|https://bioportal.bioontology.org/ontologies/NCBITAXON|https://www.ncbi.nlm.nih.gov/taxonomy|OBO: The NCBITaxon ontology is an automatic translation of the NCBI taxonomy database into obo/owl.<br/><br/>NCBI: The Taxonomy Database is a curated classification and nomenclature for all of the organisms in the public sequence databases. This currently represents about 10% of the described species of life on the planet.| -|OBOE|The Extensible Observation Ontology|environmental|CC BY 3.0|OWL|owl|reused||||https://bioportal.bioontology.org/ontologies/OBOE|https://github.com/NCEAS/oboe|https://bioportal.bioontology.org/ontologies/OBOE||BioPortal: The Extensible Observation Ontology (OBOE) is a formal ontology for capturing the semantics of scientific observation and measurement. The ontology supports researchers to add detailed semantic annotations to scientific data, thereby clarifying the inherent meaning of scientific observations| -|PATO|The Phenotype And Trait Ontology|anatomical|CC BY 3.0|OWL|owl|reused|BFO|https://obofoundry.org/ontology/pato.html|https://www.ebi.ac.uk/ols/ontologies/pato|https://bioportal.bioontology.org/ontologies/PATO|https://github.com/pato-ontology/pato/|https://bioportal.bioontology.org/ontologies/PATO||Obo & BioPortal: Phenotypic qualities (properties). This ontology can be used in conjunction with other ontologies such as GO or anatomical ontologies to refer to phenotypes. Examples of qualities are red, ectopic, high temperature, fused, small, edematous and arrested.| -|PO|Plant Ontology|biology|CC BY 4.0|OWL|owl|reused|OWL|https://obofoundry.org/ontology/po.html|https://www.ebi.ac.uk/ols/ontologies/po|https://bioportal.bioontology.org/ontologies/PO|https://github.com/Planteome/plant-ontology|https://bioportal.bioontology.org/ontologies/PO|https://www.plantontology.org|PO Consortium: The Plant Ontology is a controlled vocabulary (ontology) that describes plant anatomy and morphology and stages of development for all plants. The goal of the PO is to establish a semantic framework for meaningful cross-species queries across gene expression and phenotype data sets from plant genomics and genetics experiments.<br/><br/>BioPortal: The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data. The PO is under active development to expand to encompass terms and annotations from all plants.| -|PTO|Plant Trait Ontology|anatomical|CC BY 4.0|OWL|owl|reused|BFO|https://obofoundry.org/ontology/to.html|https://www.ebi.ac.uk/ols/ontologies/to|https://bioportal.bioontology.org/ontologies/PTO|https://github.com/Planteome/plant-trait-ontology|https://bioportal.bioontology.org/ontologies/PTO|PO, TO, PECO, PSO: https://browser.planteome.org/amigo|BioPortal: A controlled vocabulary to describe phenotypic traits in plants. Each trait is a distinguishable feature, characteristic, quality or phenotypic feature of a developing or mature plant, or a plant part.| -|SWEET|Semantic Web for Earth and Environment Technology Ontology|geo-sciences|CC0 1.0|OWL|owl|reused||||https://bioportal.bioontology.org/ontologies/SWEET|https://github.com/ESIPFed/sweet|https://bioportal.bioontology.org/ontologies/SWEET<br/><br/>http://sweetontology.net/sweetAll||BioPortal: The Semantic Web for Earth and Environmental Terminology is a mature foundational ontology that contains over 6000 concepts organized in 200 ontologies represented in OWL. Top level concepts include Representation (math, space, science, time, data), Realm (Ocean, Land Surface, Terrestrial Hydroshere, Atmosphere, etc.), Phenomena (macro-scale ecological and physical), Processes (micro-scale physical, biological, chemical, and mathematical), Human Activities (Decision, Commerce, Jurisdiction, Environmental, Research). Originally developed by NASA Jet Propulsion Labs under Rob Raskin, SWEET is now officially under the governance of the ESIP foundation.| -|GEONAMES|The Geonames geographical database|geo-sciences|CC BY 4.0|OWL|owl|reused||||||https://www.geonames.org/ontology/ontology_v3.3.rdf|http://www.geonames.org/|GeoNames: The GeoNames geographical database is available for download free of charge under a creative commons attribution license. It contains over 25 million geographical names and consists of over 11 million unique features whereof 4.8 million populated places and 13 million alternate names. All features are categorized into one out of nine feature classes and further subcategorized into one out of 645 feature codes... GeoNames is integrating geographical data such as names of places in various languages, elevation, population and others from various sources.<br/><br/>W3C: The GeoNames Ontology makes it possible to add geospatial semantic information to the Word Wide Web. All over 6.2 million geonames toponyms now have a unique URL with a corresponding RDF web service. Other services describe the relation between toponyms.<br/><br/>European Comission: The Geonames ontology provides elements of description for geographical features defined in the geonames.org data base| -|GAZ|Gazetteer. This ontology is inactive.|environment|CC0 1.0|OWL|owl|reused||https://obofoundry.org/ontology/gaz.html|https://www.ebi.ac.uk/ols/ontologies/gaz|https://bioportal.bioontology.org/ontologies/GAZ?p=summary|https://github.com/EnvironmentOntology/gaz|http://environmentontology.github.io/gaz/|https://www.ebi.ac.uk/ols/ontologies/gaz<br/><br/>http://environmentontology.github.io/gaz/|GAZ: GAZ represents places through their names using an ontological approach to promote semantic coherence. All entities in GAZ can be treated as instances of environments (see the ENVO repository).| -|DCAT|Data Catalog Vocabulary|vocabulary|W3C License|RDF|owl|reused|W3C|||https://bioportal.bioontology.org/ontologies/DCAT||DCAT V2: https://www.w3.org/TR/vocab-dcat/<br/><br/>DCAT V3: https://www.w3.org/TR/vocab-dcat-3/||W3C: DCAT 3 supersedes DCAT 2 [VOCAB-DCAT-2], but it does not make it obsolete. DCAT 3 maintains the DCAT namespace as its terms preserve backward compatibility with DCAT 2. DCAT 3 relaxes constraints and adds new classes and properties, but these changes do not break the definition of previous terms.<br/><br/>Any new implementation is expected to adopt DCAT 3, while the existing implementations do not need to upgrade to it, unless they want to use the new features. In particular, current DCAT 2 deployments that do not overlap with the DCAT 3 new features (e.g., versioning, dataset series and inverse properties) don't need to change anything to remain in conformance with DCAT 3.| -|SCHEMA||vocabulary|CC BY-SA 3.0|Various formats<br/>https://schema.org/docs/developers.html|rdf|reused||||||https://schema.org<br/>Various formats<br/>https://schema.org/docs/developers.html|https://schema.org|schema.org: These vocabularies cover entities, relationships between entities and actions, and can easily be extended through a well-documented extension model.| -|PROV-O|The PROV Ontology|ontology|W3C License||owl|reused|W3C|||||Namespace: http://www.w3.org/ns/prov#<br/><br/>OWL encoding: http://www.w3.org/TR/prov-o/|https://www.w3.org/TR/prov-o/|w3c: It provides a set of classes, properties, and restrictions that can be used to represent and interchange provenance information generated in different systems and under different contexts. It can also be specialized to create new classes and properties to model provenance information for different applications and domains.| -|DCTERMS|Dublin Core|metadata standard|CC BY 4.0||rdf|reused||||||http://purl.org/dc/terms/; http://purl.org/dc/elements/1.1/|https://www.dublincore.org/specifications/dublin-core/|dublincore.org: The Dublin Core™ metadata standard is a simple yet effective element set for describing a wide range of networked resources. The Dublin Core™ standard includes two levels: Simple and Qualified. Simple Dublin Core™ comprises fifteen elements; Qualified Dublin Core™ includes three additional elements (Audience, Provenance and RightsHolder), as well as a group of element refinements (also called qualifiers) that refine the semantics of the elements in ways that may be useful in resource discovery.| -|openDS|Open Digital Specimens|data model||||reused|||||https://github.com/DiSSCo/opends|||GitHub: openDS is a specification of Digital Specimen and other related object type definitions essential to mass digitization of natural science collections and their digital use in a new generation of infrastructure and applications. For the principal digital object types corresponding to major categories of collections and specimens’ data, openDS defines the structure and content of each object type, and the operations that can act upon them.| -|ODS|The Ontology for open Digital Specimens (ODS)||||owl|reused|OBO(?)||||https://github.com/DiSSCo/openDS/blob/master/ods-ontology/ods-ont-intro.md|||GitHub: The Ontology for open Digital Specimens (ODS) situates open Digital Specimens in the relevant OBO Foundry ontologies and extends from those roots to define the new concepts needed to support mass digitization and Digital Specimens on the Internet.| -|ABCD-EFG|Access to Biological Collection Data Extended for Geosciences.||CC BY 4.0||xsd|reused|||||||https://terms.tdwg.org/wiki/ABCD_2<br/>Currently offline<br/><br/>Schema abcdefg.xsd: https://efg.geocase.eu/sites/default/documentation/html/efg.html|ABCD Schema is a comprehensive XML-based standard for the access to and exchange of natural history collection and observational data.<br/>ABCD allows a detailed, atomized mapping of information about collection specimens and results of observations in the field. Data from any arbitrarily structured database can be mapped using freely available open source software (BioCASE provider software - www.biocase.org).| -|SKOS|Simple Knowledge Organisation System|terminologies|W3C License|SKOS|skos|only indexed||||||http://www.w3.org/2004/02/skos/core#|https://www.w3.org/2004/02/skos/<br/><br/>https://www.w3.org/TR/skos-reference/|SKOS is an area of work developing specifications and standards to support the use of knowledge organization systems (KOS) such as thesauri, classification schemes, subject heading systems and taxonomies within the framework of the Semantic Web.| -|WLMO|The WildLife Monitoring Ontology|||OWL|owl|developed||||||https://wildlive.senckenberg.de/wlmo/ontology.ttl|https://wildlive.senckenberg.de/wlmo/|The ontology developed for representing wildlife monitoring capture events, the setup within which they were observed and their results.| -|SSN|Semantic Sensor Network Ontology|sensors and their observations|W3C License|OWL|owl|reused|W3C_based, DUL aligned, OBOE_aligned, PROV-O_aligned, O&M_aligned|||https://bioportal.bioontology.org/ontologies/SSN||http://purl.oclc.org/NET/ssnx/ssn|https://www.w3.org/2005/Incubator/ssn/ssnx/ssn<br/><br/>https://service.tib.eu/ts4tib/ontologies/ssn|Bioportal: This ontology describes sensors, actuators and observations, and related concepts. It does not describe domain concepts, time, locations, etc. these are intended to be included from other ontologies via OWL imports.| -|SOSA|Sensor, Observation, Sample and Actuator (SOSA) Ontology|vocabulary|W3C License|OWL|owl|reused|W3C_based, DUL aligned, OBOE_aligned, PROV-O_aligned, O&M_aligned|||||http://liveschema.eu/dataset/lov_sosa||Ghislain Atemezing: This ontology is based on the SSN Ontology by the W3C Semantic Sensor Networks Incubator Group (SSN-XG), together with considerations from the W3C/OGC Spatial Data on the Web Working Group.<br/><br/>Article https://doi.org/10.1016/j.websem.2018.06.003 : SOSA is the result of rethinking the W3C-XG Semantic Sensor Network (SSN) ontology based on changes in scope and target audience, technical developments, and lessons learned over the past years. SOSA also acts as a replacement of SSN’s Stimulus Sensor Observation (SSO) core.<br/><br/>Observation, sampling and sample, time and more: https://www.youtube.com/watch?v=BHBU5gYAmV4| -|AO|Annotation Ontology|vocabulary|CC BY 3.0|OWL|owl|reused||||||https://code.google.com/archive/p/annotation-ontology/source/default/source|https://code.google.com/archive/p/annotation-ontology/wikis/Homepage.wiki|Google Code: Annotation Ontology (AO) is a vocabulary designed to extensively reuse existing domain ontologies (entities annotations or semantic tags) and to provide several other kind of annotations - comments, textual annotation (classic tags), notes, examples, erratum... - on potentially any kind of document (text, images, audio...) and document fragments.| -|GEOSPARQL|||OGC "open" license||owl|reused|imports Person and Organization from SCHEMA||||||http://www.opengis.net/ont/geosparql|| -|FOAF|||W3C License||owl|reused|||||||http://xmlns.com/foaf/0.1|| -|VCARD|||W3C License||owl|reused||||||http://www.w3.org/2006/vcard/ns||| -|T4FS|terms4FAIRskills||CC BY 4.0||owl|reused|imports DC, OWL, DCTERMS, OMO, RDFS, IAO, OIO, BFO, RO|||||http://purl.obolibrary.org/obo/t4fs.owl||| +A placeholder collection of ontologies, controlled vocabularies, and schemas +relevant for the NFDI4Earth Consortium created by the +[NFDI Section Metadata WG Ontology Harmonization and Mapping](https://github.com/nfdi-de/section-metadata-wg-onto/). +The working group is in the process of identifying NFDI4Earth Consortium members +appropriate for maintaining this collection. + +## Maintainers + +- [Auriol Degbelo](https://semantic.farm/orcid:0000-0001-5087-8776) + +Suggest a new addition to this collection +[here](https://github.com/biopragmatics/bioregistry/issues/new?template=add-collection-prefix.yml&collection=0000030&title=Add%20prefix%20X%20to%20collection%200000030). + +## Ontologies + +The following table comes from Semantic Farm collection +[`0000030`](https://semantic.farm/collection/0000030). + +| Prefix | Name | License | +| ---------------------------------------------- | ---------------------------------------------------------- | --------------------------------------------------------------------------------- | +| [`BCO`](https://semantic.farm/bco) | Biological Collections Ontology | CC0-1.0 | +| [`CHEBI`](https://semantic.farm/chebi) | Chemical Entities of Biological Interest | CC-BY-4.0 | +| [`dcat`](https://semantic.farm/dcat) | Data Catalog | CC-BY-4.0 | +| [`dcterms`](https://semantic.farm/dcterms) | Dublin Core Metadata Initiative Terms | | +| [`ENVO`](https://semantic.farm/envo) | Environment Ontology | CC0-1.0 | +| [`FLOPO`](https://semantic.farm/flopo) | Flora Phenotype Ontology | CC0-1.0 | +| [`foaf`](https://semantic.farm/foaf) | Friend of a Friend | CC-BY-1.0 | +| [`GAZ`](https://semantic.farm/gaz) | Gazetteer | CC0-1.0 | +| [`geonames`](https://semantic.farm/geonames) | GeoNames | CC-BY-4.0 | +| [`geosparql`](https://semantic.farm/geosparql) | GeoSPARQL | [Custom](https://www.ogc.org/license) | +| [`legacy.ao`](https://semantic.farm/legacy.ao) | Annotation Ontology | CC-BY-3.0 | +| [`n4e`](https://semantic.farm/n4e) | NFDI4Earth Ontology | CC0-1.0 | +| [`NCBITaxon`](https://semantic.farm/ncbitaxon) | NCBI Taxonomy | CC0-1.0 | +| [`oboe`](https://semantic.farm/oboe) | The Extensible Observation Ontology | CC-BY-3.0 | +| [`PATO`](https://semantic.farm/pato) | Phenotype And Trait Ontology | CC-BY-3.0 | +| [`PO`](https://semantic.farm/po) | Plant Ontology | CC-BY-4.0 | +| [`prov`](https://semantic.farm/prov) | PROV Namespace | | +| [`schema`](https://semantic.farm/schema) | Schema.org | | +| [`skos`](https://semantic.farm/skos) | Simple Knowledge Organization System | | +| [`sosa`](https://semantic.farm/sosa) | Sensor, Observation, Sample, and Actuator Ontology | [Custom](http://www.w3.org/Consortium/Legal/2015/copyright-software-and-document) | +| [`ssn`](https://semantic.farm/ssn) | Semantic Sensor Network Ontology | [Custom](http://www.w3.org/Consortium/Legal/2015/copyright-software-and-document) | +| [`sweet`](https://semantic.farm/sweet) | Semantic Web for Earth and Environment Technology Ontology | CC0-1.0 | +| [`T4FS`](https://semantic.farm/t4fs) | terms4FAIRskills | CC-BY-4.0 | +| [`tdwg.abcd`](https://semantic.farm/tdwg.abcd) | Access to Biological Collection Data Schema | | +| [`TO`](https://semantic.farm/to) | Plant Trait Ontology | CC-BY-4.0 | +| [`vcard`](https://semantic.farm/vcard) | Virtual Contact File | | +| [`wlmo`](https://semantic.farm/wlmo) | Wildlife Monitoring Ontology | CC-BY-4.0 | + +## Colophon + +This page was automatically generated on 2026-05-07 using Semantic Farm +([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +by running the following commands: + +```console +$ git clone https://github.com/nfdi-de/nfdi-sections +$ cd nfdi-sections +$ uv run scripts/update_collections.py +$ git commit -am "Update WG Onto collections" +$ git push +``` diff --git a/docs/meta/wg_onto/used-ontologies/nfdi4energy.md b/docs/meta/wg_onto/used-ontologies/nfdi4energy.md index b16335b..8cb7c7a 100644 --- a/docs/meta/wg_onto/used-ontologies/nfdi4energy.md +++ b/docs/meta/wg_onto/used-ontologies/nfdi4energy.md @@ -2,8 +2,52 @@ title: NFDI4Energy --- -Source: `/files/meta/Used_Ontologies_at_NFDI.xlsx` (sheet: NFDI4Energy) +Prefixes for ontologies relevant for the NFDI4Energy -| |Domain|License|Modularity|Format|developed / reused / only indexed / only evaluated|Used in| -|---|---|---|---|---|---|---| -|Ontology ID|Energy Systems|CC0 1.0|BFO|owl|reused|Open Energy Family & OEP| +## Maintainers + +- [Amanda Wein](https://semantic.farm/orcid:0009-0009-2960-3474) + +Suggest a new addition to this collection +[here](https://github.com/biopragmatics/bioregistry/issues/new?template=add-collection-prefix.yml&collection=0000021&title=Add%20prefix%20X%20to%20collection%200000021). + +## Ontologies + +The following table comes from Semantic Farm collection +[`0000021`](https://semantic.farm/collection/0000021), which is automatically +synced from the TIB Terminology Service collection +[`nfdi4energy`](https://service.tib.eu/terminology/collections/nfdi4energy). + +| Prefix | Name | License | +| -------------------------------------------------------------------------------- | ------------------------------------------------------------------ | ------------ | +| [`bonsai`](https://semantic.farm/bonsai) | Big Open Network of Sustainability Assessment Information Ontology | | +| [`brick`](https://semantic.farm/brick) | Brick Ontology | | +| [`cim`](https://semantic.farm/cim) | Common Information Model Ontology | | +| [`digitalconstruction.energy`](https://semantic.farm/digitalconstruction.energy) | Digital Construction Energy Ontology | | +| [`docbias`](https://semantic.farm/docbias) | Doc-Bias Ontology | | +| [`dogont`](https://semantic.farm/dogont) | Ontology Modeling for Intelligent Domotic Environments | | +| [`energymarketroles`](https://semantic.farm/energymarketroles) | Energy Market Roles ontology | | +| [`meno`](https://semantic.farm/meno) | Mid-level Energy Ontology | CC-BY-4.0 | +| [`OEO`](https://semantic.farm/oeo) | Open Energy Ontology | CC0-1.0 | +| [`openadr`](https://semantic.farm/openadr) | OpenADR ontology | | +| [`saref.ener`](https://semantic.farm/saref.ener) | SAREF4EE: the EEbus/Energy@home extension of SAREF | | +| [`saref.grid`](https://semantic.farm/saref.grid) | SAREF4GRID: an extension of SAREF for the Smart Grid domain | | +| [`sargon`](https://semantic.farm/sargon) | Smart Energy Domain Ontology | | +| [`tib.re`](https://semantic.farm/tib.re) | Retail Energy Market of Great Britain | CC-BY-SA-3.0 | +| [`udsaes.fmi`](https://semantic.farm/udsaes.fmi) | Functional Mock-up Interface Ontology | | +| [`udsaes.sms`](https://semantic.farm/udsaes.sms) | Systems, Models, and Simulation Ontology | | +| [`zbw.stw`](https://semantic.farm/zbw.stw) | Standard-Thesaurus Wirtschaft | | + +## Colophon + +This page was automatically generated on 2026-05-07 using Semantic Farm +([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +by running the following commands: + +```console +$ git clone https://github.com/nfdi-de/nfdi-sections +$ cd nfdi-sections +$ uv run scripts/update_collections.py +$ git commit -am "Update WG Onto collections" +$ git push +``` diff --git a/docs/meta/wg_onto/used-ontologies/nfdi4health.md b/docs/meta/wg_onto/used-ontologies/nfdi4health.md index 0bde5d6..ed8bcd3 100644 --- a/docs/meta/wg_onto/used-ontologies/nfdi4health.md +++ b/docs/meta/wg_onto/used-ontologies/nfdi4health.md @@ -2,82 +2,75 @@ title: NFDI4Health --- -Source: `/files/meta/Used_Ontologies_at_NFDI.xlsx` (sheet: NFDI4Health) +A placeholder collection of ontologies, controlled vocabularies, and schemas +relevant for the NFDI4Health Consortium created by the +[NFDI Section Metadata WG Ontology Harmonization and Mapping](https://github.com/nfdi-de/section-metadata-wg-onto/). +The working group is in the process of identifying NFDI4Health Consortium +members appropriate for maintaining this collection. -|Ontology ID|Ontology Name|Domain|License|Modularity|Format|developed / reused / only indexed / only evaluated|Used in|Comments / description|NFDI4Health contributions|File URL|Docs URL|SemLookP / OLS URL|FHIR URL (normative, BfArM, MII, NUM, HiGHmed, ...)|Bioportal|Github| -|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---| -|NFDI4Health MDS||Medizinische Forschung|CC BY 4.0|reuses: NFDI4Health CS MDS Provenance Data Source, NFDI4Health CS MDS Study Status, NFDI4Health CS MDS Remaining Concepts, DCTERMS, DataCite, Maelstrom, UMLS Metathesaurus, SNOMED CT, LOINC, UCUM, NCI Metathesaurus, ISO Country and Regional Codes, ISO 3166 Part 2 Country Subdivision Codes, IETF language tags, ICD-10, ICD-11, MeSH, HL7 Title Type, HL7 SPDX License, HL7 Administrative Gender, HL7 V3 Participation Type, HL7 V3 Act Relationship Type|xlsx|developed|Central Search Hub, Local Data Hub|Zentrales Metadatenschema von NFDI4Health|yes|https://repository.publisso.de/resource/frl%3A6450625|||||| -|NFDI4Health CS MDS Provenance Data Source||Medizinische Forschung|CC BY 4.0||fhir|developed|Central Search Hub, Local Data Hub, NFDI4Health MDS|Code system defining data sources in a Provenance resource.|yes|https://simplifier.net/nfdi4health-metadata-schema/nfdi4health-cs-mds-provenance-data-source|||||| -|NFDI4Health CS MDS Study Status||Medizinische Forschung|CC BY 4.0||fhir|developed|Central Search Hub, Local Data Hub, NFDI4Health MDS|Code system defining concepts about different status of a study.|yes|https://simplifier.net/nfdi4health-metadata-schema/nfdi4health-cs-mds-study-status|||||| -|NFDI4Health CS MDS Remaining Concepts||Medizinische Forschung|CC BY 4.0||fhir|developed|Central Search Hub, Local Data Hub, NFDI4Health MDS|Code system defining remaining concepts without mapping to concepts from international terminologies, ontologies, classifications, etc.|yes|https://simplifier.net/nfdi4health-metadata-schema/nfdi4health-cs-mds-remaining-concepts|||||| -|DCTERMS||Fachübergreifend|CC BY 4.0||rdf|reused|NFDI4Health MDS|Basic metadata terms|no|https://www.dublincore.org/specifications/dublin-core/dcmi-terms/|||||| -|DataCite||Fachübergreifend|||xsd|reused|NFDI4Health MDS|Advanced metadata terms|no|https://schema.datacite.org/meta/kernel-4.4/|https://doi.org/10.14454/3w3z-sa82||||| -|Maelstrom||Kohorten|Proprietary||html|reused|NFDI4Health MDS|Classifying variables used in cohorts|no|https://www.maelstrom-research.org/harmonization-search#lists?type=studies&query=study(in(Mica_study.className,HarmonizationStudy),limit(0,20))|||||| -|UMLS Metathesaurus|UMLS Metathesaurus|Medizin allgemein|Proprietary||rrf|reused|NFDI4Health MDS|Using UMLS with FHIR|no|https://www.nlm.nih.gov/research/umls/index.html|2.16.840.1.113883.6.86||||| -|SNOMED CT|SNOMED CT|Medizin allgemein|Proprietary||rf2|reused|NFDI4Health MDS|Using SNOMED CT with FHIR|no|http://snomed.info/sct|2.16.840.1.113883.6.96||||| -|LOINC|LOINC|Laborwerte|Proprietary||accdb|reused|NFDI4Health MDS|Using LOINC with FHIR|no|http://loinc.org|2.16.840.1.113883.6.1||||| -|UCUM|UCUM|Maßeinheiten|Proprietary||html|reused|NFDI4Health MDS|Using UCUM with FHIR|no|http://unitsofmeasure.org|2.16.840.1.113883.6.8||||| -|NCI Metathesaurus|NCI Metathesaurus|Fachübergreifend|Proprietary||rrf|reused|NFDI4Health MDS|Using NCI Metathesaurus with FHIR|no|http://ncimeta.nci.nih.gov|2.16.840.1.113883.3.26.1.2||||| -|ISO Country and Regional Codes|ISO Country and Regional Codes|Administrativ|Proprietary|ISOCOUNTRIES|pdf|reused|NFDI4Health MDS|Using ISO 3166 Codes with FHIR|no|urn:iso:std:iso:3166|1.0.3166.1.2.2||||| -|ISO 3166 Part 2 Country Subdivision Codes|ISO 3166 Part 2 Country Subdivision Codes|Administrativ|Proprietary||pdf|reused|NFDI4Health MDS|Two-letter code element from ISO 3166-1 followed by a separator and up to three alphanumeric characters|no|urn:iso:std:iso:3166:-2|1.0.3166.2||||| -|IETF language tags|IETF language tags|Fachübergreifend|Proprietary||txt|reused|NFDI4Health MDS|This is used for identifying language throughout FHIR. Note that usually these codes are in a code and the system is assumed|no|urn:ietf:bcp:47|2.16.840.1.113883.6.121||||| -|ICD-10|ICD-10|Krankheiten|Proprietary||claml|reused|NFDI4Health MDS|WHO and german variant|no|https://www.bfarm.de/DE/Kodiersysteme/Klassifikationen/ICD/ICD-10-GM/_node.html|ICD-10||||| -|ICD-11|ICD-11|Krankheiten|Proprietary||claml|reused|NFDI4Health MDS|Using ICD-x with FHIR|no|https://www.bfarm.de/DE/Kodiersysteme/Klassifikationen/ICD/ICD-11/uebersetzung/_node.html|2.16.840.1.113883.6.347||||| -|MeSH|MeSH|Fachübergreifend|Proprietary||rdf|reused|NFDI4Health MDS|Using MeSH in FHIR|no|https://www.ncbi.nlm.nih.gov/mesh|2.16.840.1.113883.6.177||||| -|HL7 Title Type|HL7 Title Type|Fachübergreifend|Proprietary||fhir|reused|NFDI4Health MDS|Used to express the reason and specific aspect for the variant title, such as language and specific language.|no|http://hl7.org/fhir/title-type|2.16.840.1.113883.6.121||||| -|HL7 SPDX License|HL7 SPDX License|Lizenzen|Proprietary||fhir|reused|NFDI4Health MDS|The license that applies to an Implementation Guide (using an SPDX license Identifiers, or 'not-open-source'). The binding is required but new SPDX license Identifiers are allowed to be used (https://spdx.org/licenses/).|no|http://hl7.org/fhir/spdx-license|2.16.840.1.113883.4.642.4.1027||||| -|HL7 Administrative Gender|HL7 Administrative Gender|Geschlecht|Proprietary||fhir|reused|NFDI4Health MDS|The gender of a person used for administrative purposes."|no|http://hl7.org/fhir/administrative-gender|2.16.840.1.113883.4.642.4.2||||| -|HL7 V3 Participation Type|HL7 V3 Participation Type|Fachübergreifend|Proprietary||fhir|reused|NFDI4Health MDS|A code specifying the meaning and purpose of every Participation instance. Each of its values implies specific constraints on the Roles undertaking the participation.|no|http://terminology.hl7.org/CodeSystem/v3-ParticipationType|2.16.840.1.113883.5.90||||| -|HL7 V3 Act Relationship Type|HL7 V3 Act Relationship Type|Fachübergreifend|Proprietary||fhir|reused|NFDI4Health MDS|Used in combination with NFDI4Health' defined values to express the relationship between two resources in the Value Sets NFDI4Health_VS_MDS_Relation_Type_Ids_Local_HL7V3 and NFDI4Health_VS_MDS_Relation_Type_Ids_Nfdi_Local_HL7V3|no|http://terminology.hl7.org/CodeSystem/v3-ActRelationshipType|2.16.840.1.113883.5.1002||||| -|UNDER REVIEW|||||||||||||||| -|AFEO|||||owl||||||||||| -|AGROVOC|||||skos||||||||||| -|AHOL|||||owl||||||||||| -|Alpha-ID||Freitextdiagnosen|||||||||||||| -|ATC||Arzneimittelwirkstoffe|||owl||||||||||| -|ATOL|||||owl||||||||||| -|BAO|||||owl||||||||||| -|CHEBI|||||owl||||||||||| -|CL|||||owl||||||||||| -|CLO|||||owl||||||||||| -|CMPO||||CHEBI, GO, PATO|owl||||||||||| -|COVID_VAR|||||||||||||||| -|DBSNP|||||||||||||||| -|DOID||Krankheiten||CHEBI, FOODON, NCBIT, AXON, RO, HP, UBERON, OIO, SO, DC, GENO, IAO, NCIT, DCTERMS, DISDRIV, OWL, TRANS, SYMP, IDO, OBI, RDFS, ECO, CL, EXO|owl||||||||||| -|DRG||Abrechnung mit Krankenkassen|||||||||||||| -|EBQM|||||||||||||||| -|EFO||||ORDO, MONDO, CHEBI, GO, NCBITAXON, DC, NCIT, HP, FMA, OIO, OWL, UBERON, RO, PR, FBBT, OBI, OBA, IAO, SKOS, SO, BAO, DCTERMS, CLO, HANCESTRO, OGMS, PO, IDO, ZFA, RDFS, TO, CL, PATO, MPATH, DOID, FBDV, BFO, BTO, MA, MP, OMIT, UO, WBLS|owl||||||||||| -|EOL|||||||||||||||| -|EXTRUONT|||||||||||||||| -|FOODEX2|||||||MDS Modul Ernährung||||||||| -|FOODON||||NCBITAXON, CARO, CHEBI, GO, FLOPO, NCIT, ENVO, CDNO, OIO, UBERON, DC, OBI, AGRO, IAO, COB, PECO, PR, DCTERMS, HANCESTRO, PCO, PO, RO, MSIO, ONS, ECOCORE, RDFS, DRON, PATO, BFO, SEPIO, UO, BTO, APOLLO_SV, OWL, FAO, CL, SCHEMAORG_HTTP, STATO|owl||||||||||| -|GO||||OIO, DC, IAO, DCTERMS, RDFS, RO, OWL|owl||||||||||| -|HGNC|||||owl||||||||||| -|Hl7 Vocabulary|||||||||||||||| -|HPO||Abnormalitäten||BFO aligned, OBO based|owl||||||||||| -|ICD-10 GM||Diagnosen|||||||||||||| -|ICD10||Diagnosen|||||MDS (Metadatenschema)||||||||| -|ICDO||Krebserkrankungen||BFO aligned, OBO based|||||||||||| -|IDMP||Arzneimittel|||||||||||||| -|MAELSTROM|||||||Questionnaire||||||||| -|MedDRA||Unerwünschte Ereignisse|||||||||||||| -|MESH||Verschlagwortung von Publikationen|||rdf||||||||||| -|MESHD|||||rdf||||||||||| -|MGI|||||||||||||||| -|MIRBASE|||||||||||||||| -|NCBIGENE|||||rdf||||||||||| -|NCBITAXON||||OIO, DCTERMS, IAO|owl||||||||||| -|NCIT||||OBO_based|owl||MDS||||||||| -|ONE||||CHEBI, GO, DC, NCBITAXON, OWL, OMRSE, UBERON, OBI, VO, RDFS, IAO, SO, PR, DCTERMS, CLO, OGMS, HP, IDO, SKOS, PATO, ONS, OIO, BFO, RO, APOLLO_SV, ENVO, UO, CHMO, CL|owl||MDS Ernährung||||||||| -|OPS||Prozeduren (chirurgische Eingriffe)|||||||||||||| -|OrphaNet||Seltene Erkrankungen|||||||||||||| -|RGD|||||||||||||||| -|Rote Liste||Arzneimittel|||||||||||||| -|SC2V|||||||||||||||| -|SDTM||Ergebnisdatensätze|||||||||||||| -|SNOMED|||||||MDS, Questionnaire||||||||| -|TNM||Krebserkrankungen|||||||||||||| -|UBERON||||CARO, CHEBI, RO, GO, NCBITAXON, DC, PR, OIO, SEMAPV, DCTERMS, IAO, SKOS, SO, NBO, OMO, CL, RDFS, PATO, ENVO, BFO, BSPO, OWL|owl||||||||||| -|UMLS||Metaterminologie|||||MDS||||||||| -|UNIPROT|||||||||||||||| -|XDS Value Sets|||||||||||||||| +## Maintainers + +- [Matthias Löbe](https://semantic.farm/orcid:0000-0002-2344-0426) + +Suggest a new addition to this collection +[here](https://github.com/biopragmatics/bioregistry/issues/new?template=add-collection-prefix.yml&collection=0000041&title=Add%20prefix%20X%20to%20collection%200000041). + +## Ontologies + +The following table comes from Semantic Farm collection +[`0000041`](https://semantic.farm/collection/0000041). + +| Prefix | Name | License | +| ---------------------------------------------- | ------------------------------------------------------------------------------ | ------------------------------------------------------------------------------------------------------------------ | +| [`agrovoc`](https://semantic.farm/agrovoc) | AGROVOC | CC-BY-4.0 | +| [`ahol`](https://semantic.farm/ahol) | Animal Health Ontology for Livestock | CC-BY-4.0 | +| [`atc`](https://semantic.farm/atc) | Anatomical Therapeutic Chemical Classification System | | +| [`atol`](https://semantic.farm/atol) | Animal Trait Ontology for Livestock | CC-BY-4.0 | +| [`bao`](https://semantic.farm/bao) | BioAssay Ontology | CC-BY-SA-4.0 | +| [`CHEBI`](https://semantic.farm/chebi) | Chemical Entities of Biological Interest | CC-BY-4.0 | +| [`CLO`](https://semantic.farm/clo) | Cell Line Ontology | CC-BY-3.0 | +| [`cmpo`](https://semantic.farm/cmpo) | Cellular Microscopy Phenotype Ontology | | +| [`DataCite`](https://semantic.farm/datacite) | DataCite Ontology | | +| [`dbsnp`](https://semantic.farm/dbsnp) | dbSNP | | +| [`dcterms`](https://semantic.farm/dcterms) | Dublin Core Metadata Initiative Terms | | +| [`DOID`](https://semantic.farm/doid) | Human Disease Ontology | CC0-1.0 | +| [`EFO`](https://semantic.farm/efo) | Experimental Factor Ontology | Apache-2.0 | +| [`foodex2`](https://semantic.farm/foodex2) | Food Classification and Description System (from FSA Food Type identifiers) | | +| [`FOODON`](https://semantic.farm/foodon) | The Food Ontology | CC-BY-4.0 | +| [`GO`](https://semantic.farm/go) | Gene Ontology | CC-BY-4.0 | +| [`hgnc`](https://semantic.farm/hgnc) | HUGO Gene Nomenclature Committee | CC0-1.0 | +| [`HP`](https://semantic.farm/hp) | Human Phenotype Ontology | hpo | +| [`IAO`](https://semantic.farm/iao) | Information Artifact Ontology | CC-BY-4.0 | +| [`icd10`](https://semantic.farm/icd10) | International Classification of Diseases, 10th Revision | [Custom](https://cdn.who.int/media/docs/default-source/publishing-policies/copyright/who-faq-licensing-icd-10.pdf) | +| [`icd11`](https://semantic.farm/icd11) | International Classification of Diseases, 11th Revision (Foundation Component) | CC-BY-ND-3.0-IGO | +| [`icdo`](https://semantic.farm/icdo) | International Classification of Diseases for Oncology | CC-BY-ND-3.0-IGO | +| [`loinc`](https://semantic.farm/loinc) | Logical Observation Identifiers Names and Codes | [Custom](https://uts.nlm.nih.gov/uts/assets/LicenseAgreement.pdf) | +| [`meddra`](https://semantic.farm/meddra) | Medical Dictionary for Regulatory Activities Terminology | | +| [`mesh`](https://semantic.farm/mesh) | Medical Subject Headings | CC0-1.0 | +| [`MGI`](https://semantic.farm/mgi) | Mouse Genome Informatics | CC-BY-4.0 | +| [`mirbase`](https://semantic.farm/mirbase) | miRBase pre-miRNA | public domain | +| [`NCBIGene`](https://semantic.farm/ncbigene) | NCBI Gene | | +| [`NCBITaxon`](https://semantic.farm/ncbitaxon) | NCBI Taxonomy | CC0-1.0 | +| [`NCIT`](https://semantic.farm/ncit) | NCI Thesaurus | CC-BY-4.0 | +| [`ORPHA`](https://semantic.farm/orpha) | Orphanet | CC-BY-4.0 | +| [`rgd`](https://semantic.farm/rgd) | Rat Genome Database | CC-BY-4.0 | +| [`snomedct`](https://semantic.farm/snomedct) | SNOMED CT (International Edition) | [Custom](https://uts.nlm.nih.gov/uts/assets/LicenseAgreement.pdf) | +| [`spdx`](https://semantic.farm/spdx) | Software Package Data Exchange License | CC0-1.0 | +| [`UBERON`](https://semantic.farm/uberon) | Uber Anatomy Ontology | CC-BY-3.0 | +| [`ucum`](https://semantic.farm/ucum) | Unified Code for Units of Measure | | +| [`umls`](https://semantic.farm/umls) | Unified Medical Language System Concept Unique Identifier | [Custom](https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/release/license_agreement.html) | +| [`uniprot`](https://semantic.farm/uniprot) | UniProt Protein | CC-BY-4.0 | + +## Colophon + +This page was automatically generated on 2026-05-07 using Semantic Farm +([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +by running the following commands: + +```console +$ git clone https://github.com/nfdi-de/nfdi-sections +$ cd nfdi-sections +$ uv run scripts/update_collections.py +$ git commit -am "Update WG Onto collections" +$ git push +``` diff --git a/docs/meta/wg_onto/used-ontologies/nfdi4immuno.md b/docs/meta/wg_onto/used-ontologies/nfdi4immuno.md index 412d0f5..f6490ec 100644 --- a/docs/meta/wg_onto/used-ontologies/nfdi4immuno.md +++ b/docs/meta/wg_onto/used-ontologies/nfdi4immuno.md @@ -2,7 +2,26 @@ title: NFDI4Immuno --- -Source: `/files/meta/Used_Ontologies_at_NFDI.xlsx` (sheet: NFDI4Immuno) +This consortia has not yet created an ontology list. -|Ontology ID|Domain|License|Modularity|Format|developed / reused / only indexed / only evaluated|Used in| -|---|---|---|---|---|---|---| +## Maintainers + +- [Ulrik Stervbo](https://semantic.farm/orcid:0000-0002-2831-8868) +- [Sebastian Böhm](https://semantic.farm/orcid:0009-0006-4599-6309) + +Suggest a new addition to this collection +[here](https://github.com/biopragmatics/bioregistry/issues/new?template=add-collection-prefix.yml&collection=0000043&title=Add%20prefix%20X%20to%20collection%200000043). + +## Colophon + +This page was automatically generated on 2026-05-07 using Semantic Farm +([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +by running the following commands: + +```console +$ git clone https://github.com/nfdi-de/nfdi-sections +$ cd nfdi-sections +$ uv run scripts/update_collections.py +$ git commit -am "Update WG Onto collections" +$ git push +``` diff --git a/docs/meta/wg_onto/used-ontologies/nfdi4ing.md b/docs/meta/wg_onto/used-ontologies/nfdi4ing.md index 192002e..168650b 100644 --- a/docs/meta/wg_onto/used-ontologies/nfdi4ing.md +++ b/docs/meta/wg_onto/used-ontologies/nfdi4ing.md @@ -2,56 +2,142 @@ title: NFDI4Ing --- -Source: `/files/meta/Used_Ontologies_at_NFDI.xlsx` (sheet: NFDI4Ing) - -|Ontology ID|Ontology name|Domain|License|Modularity|Format|Used in|Comment|developed / reused / only indexed / only evaluated| -|---|---|---|---|---|---|---|---|---| -|BFO|Basic Formal Ontology|top-level ontology|CC BY 4.0|2.0 classes only OBO backbone|owl|~300 ontologies & ~50 organizations, PubChem, indexed by NFDI4Ing Terminology Service||reused| -|IAO|Information Artefact Ontology|Information artifacts|CC BY 4.0|BFO aligned, OBO based|owl|OBO Foundry, Allotrope™, PubChem, ISA tools, indexed by NFDI4Ing Terminology Service||reused| -|EMMO|Elementary Multiperspective Material Ontology (EMMO)|top-level ontology|CC BY 4.0||owl|indexed by NFDI4Ing Terminology Service||reused| -|PROV-O|The PROV Ontology|provenance information|W3C License|W3C_based|owl|indexed by NFDI4Ing Terminology Service||reused| -|DCTERMS|DCMI Metadata Terms|General|CC BY 4.0||rdf|indexed by NFDI4Ing Terminology Service||reused| -|SHACL|W3C Shapes Constraint Language (SHACL) Vocabulary|information technology|W3C Document License/ Copyright © 2017 W3C® (MIT, ERCIM, Keio, Beihang). W3C liability, trademark and document use rules apply.|||indexed by NFDI4Ing Terminology Service||only indexed| -|TEMA|Thesaurus Technology and Management (TEMA)|Engineering, Management|Proprietary||owl|indexed by NFDI4Ing Terminology Service||reused| -|PhySH|Physics Subject Headings|Physics|CC0 1.0||owl|indexed by NFDI4Ing Terminology Service||reused| -|FINDEX Bau|FINDEX Bau als SKOS-Thesaurus. Facettenartiges Indexierungssystem für das Bauwesen|Civil Engineering|CC BY-NC-SA 4.0||skos|indexed by NFDI4Ing Terminology Service||reused| -|FINDEX Raum|FINDEX Raum als SKOS-Thesaurus. Facettenartiges Indexierungssystem für Raumordnung, Städtebau, Wohnungswesen|Regional Planning/Spatial Planning|CC BY-NC-SA 4.0||skos|indexed by NFDI4Ing Terminology Service||reused| -|listdb|ListDB-Ontologie|Traffic Engineering|CC BY 4.0||owl|indexed by NFDI4Ing Terminology Service||developed| -|QUDT|Quantities, Units, Dimensions and Types<br/>(QUDT)|units of measure, quantity kind, dimensions and data types|CC BY 4.0||owl|used by m4i and AIMS||reused| -|pims-ii|PIMS interoperability infrastructure (PIMS-II)|cognitive processes, epistemic metadata, mid/top level|LGPL 3.0||owl|used by m4i||reused| -|SciMesh||empirical science|CC BY-NC-SA 4.0|||||developed| -|SEPIO||Scientific Evidence and Provenance Information|CC BY 4.0|BFO aligned, OBO based (imports from OBI, RO, IAO, COB, PATO, STATO), partial PROV-O alignement (e.g. Agent & Activity)|owl|indexed by NFDI4Ing Terminology Service||only indexed| -|OEO|Open Energy Ontology|Energy System Modelling|CC 0|BFO, IAO, RO, UO|owl|indexed by NFDI4Ing Terminology Service||only indexed| -|DUO|Data Use Ontology|data management|CC BY 4.0|BFO aligned, OBO based|owl|indexed by NFDI4Ing Terminology Service||only indexed| -|UO|Unit Ontology|General, Physics, Life Sciences, biology, Earth sciences|CC BY 2.0|OBO_based|owl|indexed by NFDI4Ing Terminology Service||only indexed| -|MV|MobiVoc Open Mobility Vocabulary 1.1.4|traffic engineering|CC BY 4.0||owl|indexed by NFDI4Ing Terminology Service||only indexed| -|SIO|Semanticscience Integrated Ontology (SIO)|General|CC BY 4.0|BFO alignment possible|owl|indexed by NFDI4Ing Terminology Service||only indexed| -|SWO|Software Ontology|software products|CC BY 4.0|BFO aligned, OBO based|owl|indexed by NFDI4Ing Terminology Service||only indexed| -|PREMIS3|PREMIS OWL Ontology|culture, digital preservation|CC BY 4.0||owl|indexed by NFDI4Ing Terminology Service||only indexed| -|OM|Ontology of units of Measure (OM)|measurements, metrology|CC BY 4.0||owl|indexed by NFDI4Ing Terminology Service||only indexed| -|SOSA|Sensor, Observation, Sample, and Actuator (SOSA) Ontology|measurement technology|W3C License|W3C_based, DUL aligned, OBOE_aligned, PROV-O_aligned, O&M_aligned|owl|indexed by NFDI4Ing Terminology Service||only indexed| -|SOSA|Semantic Sensor Network Ontology|measurement technology|W3C License|W3C_based, DUL aligned, OBOE_aligned, PROV-O_aligned, O&M_aligned|owl|indexed by NFDI4Ing Terminology Service||only indexed| -|SSN-SYSTEM|System capabilities, operating ranges, and survival ranges ontology|measurement technology|W3C License|W3C_based, DUL aligned, OBOE_aligned, PROV-O_aligned, O&M_aligned|owl|indexed by NFDI4Ing Terminology Service||only indexed| -|BattINFO|Battery Interface Ontology (BattINFO) 0.3.0|electrical engineering|CC BY 4.0||owl|indexed by NFDI4Ing Terminology Service||only indexed| -|IIRDS-CORE|IIRDS CORE Ontology|technical documentation, information management|CC BY-ND 4.0||owl|indexed by NFDI4Ing Terminology Service||only indexed| -|IIRDS-Machinery|IIRDS Machinery Ontology|technical documentation, information management|CC BY-ND 4.0||owl|indexed by NFDI4Ing Terminology Service||only indexed| -|IIRDS-Software|IIRDS Software Ontology|technical documentation, information management|CC BY-ND 4.0||owl|indexed by NFDI4Ing Terminology Service||only indexed| -|MDO|Materials Design Ontology|Material Science|MIT License|||indexed by NFDI4Ing Terminology Service||only indexed| -|SD|The Software Description Ontology|Computer Science|CC BY 2.0|||indexed by NFDI4Ing Terminology Service||only indexed| -|Basisklassifikation|Basisklassifikation|General (Subject Classification)|CC 0|||indexed by NFDI4Ing Terminology Service||only indexed| -|CC-REL|Describing Copyright in RDF - Creative Commons Rights Expression Language|Law|CC BY 4.0|||indexed by NFDI4Ing Terminology Service||only indexed| -|PaNET|The Photon and Neutron Experimental Techniques Ontology|physics|CC BY 4.0|||indexed by NFDI4Ing Terminology Service||only indexed| -|OAI-ORE|The OAI ORE terms vocabulary|information technology|CC BY-SA|||indexed by NFDI4Ing Terminology Service||only indexed| -|Digital Reference||semiconductors|GNU General Public License v3.0|||indexed by NFDI4Ing Terminology Service||only indexed| -|VSSo Core: Vehicle Signal Specification Core Ontology. W3C First Public Working Draft 03 March 2022||Traffic Engineering|CC BY 4.0|||indexed by NFDI4Ing Terminology Service||only indexed| -|FID BAUdigital Subject Headings||Civil Engineering, Architecture|CC BY 4.0|||indexed by NFDI4Ing Terminology Service||only indexed| -|Unified Astronomy Thesaurus (UAT)||Astronomy|Creative Commons Attribution-ShareAlike 3.0 Unported License|||indexed by NFDI4Ing Terminology Service||only indexed| -|Interdisziplinäre Forschungsfeldklassifikation||General (Subject Classification)|CC BY-SA 4.0|||indexed by NFDI4Ing Terminology Service||only indexed| -|Building Topology Ontology||Civil Engineering|CC BY 1.0|||indexed by NFDI4Ing Terminology Service||only indexed| -|Digital Construction Energy (dices)||Civil Engineering|CC BY 4.0|||indexed by NFDI4Ing Terminology Service||only indexed| -|Digital Construction Lifecycle (dicl)||Civil Engineering|CC BY 4.0|||indexed by NFDI4Ing Terminology Service||only indexed| -|Digital Construction Occupancy||Civil Engineering|CC BY 4.0|||indexed by NFDI4Ing Terminology Service||only indexed| -|Data Privacy Vocabulary (DPV)||Law|W3C Community Contributor License Agreement (CLA)|||indexed by NFDI4Ing Terminology Service||only indexed| -|FAIR Vocabulary||General|CC BY 4.0|||indexed by NFDI4Ing Terminology Service||only indexed| -|M4I||mid-level ontology|CC BY 4.0|partial BFO, PROV, DCAT, FOAF and SCHEMA alignment|owl|indexed by NFDI4Ing Terminology Service|developed by NFDI4Ing|developed| -|EDAM||Life-sciences & data management|CC BY 4.0|OBO mapping possible|owl|EMBOSS, Bio-jETI, indexed by NFDI4Ing Terminology Service||reused| +A collection of ontologies, controlled vocabularies, and schemas relevant for +engineering and the [NFDI4Ing Consortium](https://nfdi4ing.de). Ontologies are +chronologically imported from the corresponding +[TIB Terminology Service collection](https://service.tib.eu/terminology/collections/nfdi4ing). + +## Maintainers + +- [Dorothea Iglezakis](https://semantic.farm/orcid:0000-0002-8524-0569) +- [Giacomo Lanza](https://semantic.farm/orcid:0000-0002-2239-3955) +- [Susanne Arndt](https://semantic.farm/orcid:0000-0002-1019-9151) + +Suggest a new addition to this collection +[here](https://github.com/biopragmatics/bioregistry/issues/new?template=add-collection-prefix.yml&collection=0000022&title=Add%20prefix%20X%20to%20collection%200000022). + +## Ontologies + +The following table comes from Semantic Farm collection +[`0000022`](https://semantic.farm/collection/0000022), which is automatically +synced from the TIB Terminology Service collection +[`nfdi4ing`](https://service.tib.eu/terminology/collections/nfdi4ing). + +| Prefix | Name | License | +| -------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------ | --------------------------------------------------------------------------------- | +| [`afo`](https://semantic.farm/afo) | Allotrope Merged Ontology Suite | [Custom](http://purl.allotrope.org/voc/copyright) | +| [`atomistic`](https://semantic.farm/atomistic) | Atomistic | CC-BY-4.0 | +| [`battinfo`](https://semantic.farm/battinfo) | Battery Interface Ontology | | +| [`BFO`](https://semantic.farm/bfo) | Basic Formal Ontology | CC-BY-4.0 | +| [`bonsai`](https://semantic.farm/bonsai) | Big Open Network of Sustainability Assessment Information Ontology | | +| [`bot`](https://semantic.farm/bot) | Building Topology Ontology | | +| [`brick`](https://semantic.farm/brick) | Brick Ontology | | +| [`building`](https://semantic.farm/building) | Building Ontology | | +| [`cc`](https://semantic.farm/cc) | Creative Commons Rights Expression Language | CC0-1.0 | +| [`commoncoreontology`](https://semantic.farm/commoncoreontology) | Common Core Ontologies | CC-BY-4.0 | +| [`condo`](https://semantic.farm/condo) | The COnCEPT upper-level Design Ontology | | +| [`cora`](https://semantic.farm/cora) | Core Ontology for Robotics and Automation | | +| [`credit`](https://semantic.farm/credit) | Contributor Roles Taxonomy | CC-BY-4.0 | +| [`dcterms`](https://semantic.farm/dcterms) | Dublin Core Metadata Initiative Terms | | +| [`dfg.fo`](https://semantic.farm/dfg.fo) | DFG Classification of Subject Areas Ontology - 2020-2024 | CC-BY-4.0 | +| [`digitalconstruction.energy`](https://semantic.farm/digitalconstruction.energy) | Digital Construction Energy Ontology | | +| [`digitalconstruction.lifecycle`](https://semantic.farm/digitalconstruction.lifecycle) | Digital Construction Lifecycle (dicl) | | +| [`digitalconstruction.occupancy`](https://semantic.farm/digitalconstruction.occupancy) | Digital Construction Occupancy | | +| [`dogont`](https://semantic.farm/dogont) | Ontology Modeling for Intelligent Domotic Environments | | +| [`dpvocab`](https://semantic.farm/dpvocab) | Data Privacy Vocabulary | W3C-20150513 | +| [`DUO`](https://semantic.farm/duo) | Data Use Ontology | CC-BY-4.0 | +| [`edam`](https://semantic.farm/edam) | EDAM Ontology | CC-BY-SA-4.0 | +| [`emmo`](https://semantic.farm/emmo) | Elementary Multiperspective Material Ontology | CC-BY-4.0 | +| [`fabio`](https://semantic.farm/fabio) | FaBiO, the FRBR-aligned Bibliographic Ontology | CC-BY-4.0 | +| [`fair`](https://semantic.farm/fair) | FAIR Vocabulary | | +| [`fidbaudigital.subject`](https://semantic.farm/fidbaudigital.subject) | FID BAUdigital Subject Headings | | +| [`fiesta.iot`](https://semantic.farm/fiesta.iot) | FIESTA-IoT Ontology | | +| [`findex.bau`](https://semantic.farm/findex.bau) | FINDEX Bau as a SKOS Thesaurus - Facetted Indexing System for Civil Engineering | | +| [`findex.raum`](https://semantic.farm/findex.raum) | FINDEX Raum | | +| [`ftonto`](https://semantic.farm/ftonto) | Fischertechnik Ontology | | +| [`geosparql`](https://semantic.farm/geosparql) | GeoSPARQL | [Custom](https://www.ogc.org/license) | +| [`gist`](https://semantic.farm/gist) | gist | CC-BY-4.0 | +| [`IAO`](https://semantic.farm/iao) | Information Artifact Ontology | CC-BY-4.0 | +| [`idsa`](https://semantic.farm/idsa) | International Data Spaces Information Model | | +| [`iirds.core`](https://semantic.farm/iirds.core) | International Standard for Intelligent Information Request and Delivery Core Ontology | | +| [`iirds.mch`](https://semantic.farm/iirds.mch) | International Standard for Intelligent Information Request and Delivery Machinery Ontology | | +| [`iirds.sft`](https://semantic.farm/iirds.sft) | International Standard for Intelligent Information Request and Delivery Software Ontology | | +| [`infosecsos`](https://semantic.farm/infosecsos) | InfoSecSoS Ontology | | +| [`iofcore`](https://semantic.farm/iofcore) | Industrial Ontology Foundry (IOF) Core Ontology | | +| [`kdsf.ffk`](https://semantic.farm/kdsf.ffk) | Interdisziplinäre Forschungsfeldklassifikation | CC-BY-SA-4.0 | +| [`kit.mtxx`](https://semantic.farm/kit.mtxx) | Vocabulary of Materials Tribology Lab at KIT | | +| [`kpio`](https://semantic.farm/kpio) | Key Performance Indicator ontology | | +| [`listdb.onto`](https://semantic.farm/listdb.onto) | ListDB Ontology | | +| [`m4i`](https://semantic.farm/m4i) | Metadata4Ing | CC-BY-4.0 | +| [`mathmoddb`](https://semantic.farm/mathmoddb) | MathModDB Ontology and Knowledge Graph for Mathematical Models | CC-BY-4.0 | +| [`mobivoc`](https://semantic.farm/mobivoc) | MobiVoc Open Mobility Vocabulary 1.1.4 | | +| [`modsci`](https://semantic.farm/modsci) | Modern Science Ontology | | +| [`OEO`](https://semantic.farm/oeo) | Open Energy Ontology | CC0-1.0 | +| [`okn.sd`](https://semantic.farm/okn.sd) | The Software Description Ontology | | +| [`om`](https://semantic.farm/om) | Ontology of units of Measure | CC-BY-4.0 | +| [`panet`](https://semantic.farm/panet) | PaN Experimental technique | CC-BY-4.0 | +| [`physh`](https://semantic.farm/physh) | Physics Subject Headings | CC0-1.0 | +| [`pmdco`](https://semantic.farm/pmdco) | Platform Material Digital Core Ontology | CC-BY-4.0 | +| [`polymat`](https://semantic.farm/polymat) | PolyMat Ontology | | +| [`pror`](https://semantic.farm/pror) | PRO Research: An ontology for describing RDM-Policies in a structured way | | +| [`prov`](https://semantic.farm/prov) | PROV Namespace | | +| [`rosetta`](https://semantic.farm/rosetta) | The ROSETTA ontology of industrial robotics devices and robotic skills. | | +| [`saref`](https://semantic.farm/saref) | Smart Applications Reference ontology | [Custom](https://forge.etsi.org/etsi-software-license) | +| [`saref.auto`](https://semantic.farm/saref.auto) | SAREF4AUTO: an extension of SAREF for the automotive domain | | +| [`saref.building`](https://semantic.farm/saref.building) | SAREF extension for building devices | | +| [`saref.ehaw`](https://semantic.farm/saref.ehaw) | SAREF4EHAW: an extension of SAREF for eHealth Ageing Well domain | [Custom](https://forge.etsi.org/etsi-software-license) | +| [`saref.ener`](https://semantic.farm/saref.ener) | SAREF4EE: the EEbus/Energy@home extension of SAREF | | +| [`saref.environment`](https://semantic.farm/saref.environment) | SAREF extension for environment | | +| [`saref.industry`](https://semantic.farm/saref.industry) | SAREF4INMA: an extension of SAREF for the industry and manufacturing domain | | +| [`saref.lift`](https://semantic.farm/saref.lift) | SAREF4LIFT: an extension of SAREF for the Smart Lifts domain | | +| [`saref.system`](https://semantic.farm/saref.system) | SAREF4SYST: an extension of SAREF for typology of systems and their inter-connections | | +| [`saref.water`](https://semantic.farm/saref.water) | SAREF extension for water | | +| [`saref.wearable`](https://semantic.farm/saref.wearable) | SAREF4WEAR: an extension of SAREF for Wearables | | +| [`SEPIO`](https://semantic.farm/sepio) | Scientific Evidence and Provenance Information Ontology | CC-BY-3.0 | +| [`sh`](https://semantic.farm/sh) | Shapes Constraint Language | | +| [`si`](https://semantic.farm/si) | International System of Units Reference Point | CC-BY-3.0-IGO | +| [`SIO`](https://semantic.farm/sio) | Semanticscience Integrated Ontology | CC-BY-4.0 | +| [`sosa`](https://semantic.farm/sosa) | Sensor, Observation, Sample, and Actuator Ontology | [Custom](http://www.w3.org/Consortium/Legal/2015/copyright-software-and-document) | +| [`ssn`](https://semantic.farm/ssn) | Semantic Sensor Network Ontology | [Custom](http://www.w3.org/Consortium/Legal/2015/copyright-software-and-document) | +| [`ssn.system`](https://semantic.farm/ssn.system) | System capabilities, operating ranges, and survival ranges ontology | [Custom](http://www.w3.org/Consortium/Legal/2015/copyright-software-and-document) | +| [`sweet`](https://semantic.farm/sweet) | Semantic Web for Earth and Environment Technology Ontology | CC0-1.0 | +| [`SWO`](https://semantic.farm/swo) | Software ontology | CC-BY-4.0 | +| [`T4FS`](https://semantic.farm/t4fs) | terms4FAIRskills | CC-BY-4.0 | +| [`tib.bk`](https://semantic.farm/tib.bk) | Basic Classification | CC0-1.0 | +| [`tib.bo`](https://semantic.farm/tib.bo) | Base Ontology | | +| [`tib.dot`](https://semantic.farm/tib.dot) | Damage Topology Ontology | | +| [`tib.dr`](https://semantic.farm/tib.dr) | Digital Reference | | +| [`tib.gpo`](https://semantic.farm/tib.gpo) | General Process Ontology | CC-BY-4.0 | +| [`tib.hpont`](https://semantic.farm/tib.hpont) | Heat Pump Ontology | | +| [`tib.ifc`](https://semantic.farm/tib.ifc) | Industrial Foundational Classes | | +| [`tib.io`](https://semantic.farm/tib.io) | Information Objects Ontology | | +| [`tib.ioc`](https://semantic.farm/tib.ioc) | IOC: Internet of Construction Ontology | | +| [`tib.lis`](https://semantic.farm/tib.lis) | Industrial Data Ontology | | +| [`tib.mat`](https://semantic.farm/tib.mat) | Material properties ontology | | +| [`tib.mdo`](https://semantic.farm/tib.mdo) | Materials Design Ontology - Full | | +| [`tib.mdv`](https://semantic.farm/tib.mdv) | Simple Knowledge Organization System (SKOS) version of Materials Data Vocabulary | | +| [`tib.mt`](https://semantic.farm/tib.mt) | Mobility Theme | | +| [`tib.n0`](https://semantic.farm/tib.n0) | The Audio Commons Ontology | | +| [`tib.ofm`](https://semantic.farm/tib.ofm) | Ontology for manufacturing and logistics | | +| [`tib.sto`](https://semantic.farm/tib.sto) | Standards Ontology | | +| [`tib.tso`](https://semantic.farm/tib.tso) | TUBES system ontology | | +| [`tribain`](https://semantic.farm/tribain) | Tribology Ontology for Artificial Intelligence | | +| [`uat`](https://semantic.farm/uat) | Unified Astronomy Thesaurus | CC-BY-SA-3.0 | +| [`UO`](https://semantic.farm/uo) | Units of measurement ontology | CC-BY-3.0 | +| [`vssocore`](https://semantic.farm/vssocore) | Vehicle Signal Specification Core Ontology | | +| [`woc.ontology`](https://semantic.farm/woc.ontology) | Code Ontology | | +| [`wot.td`](https://semantic.farm/wot.td) | Thing Description Ontology | | + +## Colophon + +This page was automatically generated on 2026-05-07 using Semantic Farm +([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +by running the following commands: + +```console +$ git clone https://github.com/nfdi-de/nfdi-sections +$ cd nfdi-sections +$ uv run scripts/update_collections.py +$ git commit -am "Update WG Onto collections" +$ git push +``` diff --git a/docs/meta/wg_onto/used-ontologies/nfdi4memory.md b/docs/meta/wg_onto/used-ontologies/nfdi4memory.md index d87a9ae..c5665ae 100644 --- a/docs/meta/wg_onto/used-ontologies/nfdi4memory.md +++ b/docs/meta/wg_onto/used-ontologies/nfdi4memory.md @@ -2,31 +2,58 @@ title: NFDI4Memory --- -Source: `/files/meta/Used_Ontologies_at_NFDI.xlsx` (sheet: NFDI4Memory) - -|BARTOC URI|Ontology ID|Domain|License|Modularity|Format|developed / reused / only indexed / only evaluated|Used in|Disclaimer: *Die Erfassung der Vokabulare/Ontologien in 4Memory läuft gerade erst an und wird erst 2024 abgeschlossen sein.| -|---|---|---|---|---|---|---|---|---| -|http://bartoc.org/en/node/20291|CIDOC-CRM|Conceptual Reference Model (CRM)|CC BY 4.0||owl|reused|| -|none|LIDO|Museen|CC BY 4.0|based on CIDOC-CRM, CDWA, museumdat, and SPECTRUM|xsd|reused|International Committee for Documentation| -||OntoME|Referenzmodell|CC BY 4.0|CIDOC-CRM|rdf|reused|Data for History| -|http://bartoc.org/en/node/17946|EDM|cultural heritage data|EUPL|ORE, DOAP, SVCS, CC|owl|reused|Europeana|RDF Model| -|none (not one ontology)|TEI|Textual Documents|CC BY 3.0||xsd|reused|| -|http://bartoc.org/en/node/20435|GOV|Geschichtliches Ortsverzeichnis|CC0 1.0|Teilweise maps_to: "GND, GEONAMES, Bundesamt für Geodäsie, WIKIDATA"|rdf|reused|Verein für Computergenealogie| -|http://bartoc.org/en/node/970|ISCO|International Standard Classifcation of Occupations|CC0 1.0|ISCED-ISCO, maps_to: "KldB"||reused|International Labour Organization| -|https://bartoc.org/en/node/18800|HISCO|History of Work|CC0 1.0|ISCO-68||reused|International Institute of Social History| -|http://bartoc.org/en/node/20452|KldB|Klassifikation der Berufe 2010 / 2020|CC0 1.0|Teilweise maps_to: "GND, GEONAMES, Bundesamt für Geodäsie, WIKIDATA"||reused|Bundesagentur für Arbeit| -|http://bartoc.org/en/node/1674|GEONAMES||CC BY 4.0||owl|reused||| -|https://bartoc.org/en/node/75|AAT|Culture: Art & Architecture|ODC-By 1.0||skos|reused||partOf Getty Vocabularies| -|https://bartoc.org/en/node/109|TGN|General: Geographic Names|ODC-By 1.0||skos|reused||partOf Getty Vocabularies| -|https://bartoc.org/en/node/94|CONA|Culture: Cultural Objects|ODC-By 1.0||skos|reused||partOf Getty Vocabularies| -|https://bartoc.org/en/node/118|ULAN|Culture: Artist Names & Information|ODC-By 1.0||skos|reused||partOf Getty Vocabularies| -|none|IA|Culture: proper names, relationships, and dates for iconographical narratives, religious or fictional characters, historical events, names of literary works and performing art|ODC-By 1.0||skos|reused||partOf Getty Vocabularies| -|https://bartoc.org/en/node/18498|CDWA|Culture: set of guidelines and cataloging rules for the description of art, architecture, and other cultural works|ODC-By 1.0||skos|reused||partOf Getty Vocabularies| -|http://bartoc.org/en/node/459|Iconclass||||skos|reused|| -|http://bartoc.org/en/node/20437|OhdAB|Ontologie der historischen, deutschsprachigen Amts- und Berufsbezeichnungen|CC BY-SA 4.0|Teilweise maps_to: "GND, GEONAMES, Bundesamt für Geodäsie, WIKIDATA"|rdf|reused|Historisches Datenzentrum Sachsen-Anhalt|https://www.geschichte.uni-halle.de/struktur/hist-data/ontologie/| -|multiple|Factgrid|Wikibase|CC0 1.0|maps_to: "OhdAB|rdf|reused|| -|http://bartoc.org/en/node/1940|WIKIDATA||CC0 1.0||rdf|reused|| -|http://bartoc.org/en/node/430|GND|Gemeinsame Normdatei|CC0 1.0||rdf|reused|| -|http://bartoc.org/en/node/704|Tadirah|Taxonomy of Digital Research Activities in the Humanities|CC0 1.0|||reused|| -|none|NFDICO|Research Information for NFDI consortia|CC BY 4.0|imports SCHEMA, maps_to: "DCAT, DOAP, FOAF, FABIO, SD, VCARD, VIVO, SWO, WIKIDATA, ORG, FRAPO, MODSCI, DBO, SCHEMA, DCTERMS, IAO, OBI"|owl|reused|NFDI4Culture, NFDI-MatWerk, NFDI4DataScience| -||https://ise-fizkarlsruhe.github.io/nfdicore/||||||| +A placeholder collection of ontologies, controlled vocabularies, and schemas +relevant for the NFDI4Memory Consortium created by the +[NFDI Section Metadata WG Ontology Harmonization and Mapping](https://github.com/nfdi-de/section-metadata-wg-onto/). +The working group is in the process of identifying NFDI4Memory Consortium +members appropriate for maintaining this collection. + +## Maintainers + +- [Tabea Tietz](https://semantic.farm/orcid:0000-0002-1648-1684) + +Suggest a new addition to this collection +[here](https://github.com/biopragmatics/bioregistry/issues/new?template=add-collection-prefix.yml&collection=0000037&title=Add%20prefix%20X%20to%20collection%200000037). + +## Ontologies + +The following table comes from Semantic Farm collection +[`0000037`](https://semantic.farm/collection/0000037). + +| Prefix | Name | License | +| ------------------------------------------------------------ | ----------------------------------------------------------------------------------- | ---------- | +| [`cidoc.crm`](https://semantic.farm/cidoc.crm) | CIDOC Conceptual Reference Model | | +| [`edm`](https://semantic.farm/edm) | Europeana Data Model vocabulary | | +| [`factgrid`](https://semantic.farm/factgrid) | FactGrid | | +| [`geonames`](https://semantic.farm/geonames) | GeoNames | CC-BY-4.0 | +| [`getty.att`](https://semantic.farm/getty.att) | Art and Architecture Thesaurus | ODC-By-1.0 | +| [`getty.cona`](https://semantic.farm/getty.cona) | Cultural Objects Names Authority | ODC-By-1.0 | +| [`getty.ia`](https://semantic.farm/getty.ia) | Getty Iconography Authority | | +| [`getty.tgn`](https://semantic.farm/getty.tgn) | Getty Thesaurus of Geographic Names | ODC-By-1.0 | +| [`getty.ulan`](https://semantic.farm/getty.ulan) | Union List of Artist Names | ODC-By-1.0 | +| [`gnd`](https://semantic.farm/gnd) | Gemeinsame Normdatei | CC0-1.0 | +| [`gov.object`](https://semantic.farm/gov.object) | Historic Geo Information System Object | | +| [`hisco`](https://semantic.farm/hisco) | Historical International Standard Classification of Occupations | | +| [`iconclass`](https://semantic.farm/iconclass) | Iconclass Classification | ODbL-1.0 | +| [`kldb`](https://semantic.farm/kldb) | German classification of occupations | | +| [`lido`](https://semantic.farm/lido) | Lightweight Information Describing Objects | CC-BY-4.0 | +| [`nfdi.core`](https://semantic.farm/nfdi.core) | NFDI Core Ontology | CC0-1.0 | +| [`nfdi4culture.cto`](https://semantic.farm/nfdi4culture.cto) | NFDI4Culture Ontology | CC0-1.0 | +| [`ohdab`](https://semantic.farm/ohdab) | Ontology of the historical German-language nomenclature for offices and professions | | +| [`ontome`](https://semantic.farm/ontome) | Ontology Management Environment | CC-BY-4.0 | +| [`tadirah`](https://semantic.farm/tadirah) | Taxonomy of Digital Research Activities in the Humanities | CC0-1.0 | +| [`wikidata`](https://semantic.farm/wikidata) | Wikidata | CC0-1.0 | + +## Colophon + +This page was automatically generated on 2026-05-07 using Semantic Farm +([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +by running the following commands: + +```console +$ git clone https://github.com/nfdi-de/nfdi-sections +$ cd nfdi-sections +$ uv run scripts/update_collections.py +$ git commit -am "Update WG Onto collections" +$ git push +``` diff --git a/docs/meta/wg_onto/used-ontologies/nfdi4microbiota.md b/docs/meta/wg_onto/used-ontologies/nfdi4microbiota.md index 73a8103..375162c 100644 --- a/docs/meta/wg_onto/used-ontologies/nfdi4microbiota.md +++ b/docs/meta/wg_onto/used-ontologies/nfdi4microbiota.md @@ -2,7 +2,27 @@ title: NFDI4Microbiota --- -Source: `/files/meta/Used_Ontologies_at_NFDI.xlsx` (sheet: NFDI4Microbiota) +This consortia has not yet created an ontology list. -|Ontology ID|Domain|License|Modularity|Format|developed / reused / only indexed / only evaluated|Used in| -|---|---|---|---|---|---|---| +## Maintainers + +- [Anandhi Iyappan](https://semantic.farm/orcid:0000-0002-5571-4962) +- [Noriko Cassman](https://semantic.farm/orcid:0000-0003-1655-0931) +- [Maja Magel](https://semantic.farm/orcid:0009-0004-2517-0791) + +Suggest a new addition to this collection +[here](https://github.com/biopragmatics/bioregistry/issues/new?template=add-collection-prefix.yml&collection=0000042&title=Add%20prefix%20X%20to%20collection%200000042). + +## Colophon + +This page was automatically generated on 2026-05-07 using Semantic Farm +([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +by running the following commands: + +```console +$ git clone https://github.com/nfdi-de/nfdi-sections +$ cd nfdi-sections +$ uv run scripts/update_collections.py +$ git commit -am "Update WG Onto collections" +$ git push +``` diff --git a/docs/meta/wg_onto/used-ontologies/nfdi4objects.md b/docs/meta/wg_onto/used-ontologies/nfdi4objects.md index 38979cb..7066696 100644 --- a/docs/meta/wg_onto/used-ontologies/nfdi4objects.md +++ b/docs/meta/wg_onto/used-ontologies/nfdi4objects.md @@ -2,23 +2,91 @@ title: NFDI4Objects --- -Source: `/files/meta/Used_Ontologies_at_NFDI.xlsx` (sheet: NFDI4Objects) - -|BARTOC URI|Ontology ID|Domain|License|Modularity|Format|developed / reused / only indexed / only evaluated|Used in|Note| -|---|---|---|---|---|---|---|---|---| -|http://bartoc.org/en/node/20291|CIDOC-CRM|cultural heritage and museum documentation|CC BY 4.0|Abstract data model|owl|reused||Upper Ontology| -|none/multiple|LIDO|museums|CC BY 4.0|based on CIDOC-CRM, CDWA, museumdat, and SPECTRUM|xsd|reused|Museum databases|Data format| -|http://bartoc.org/en/node/17946|EDM|cultural heritage data|EUPL|based on CIDOC-CRM, Dublin Core, SKOS und OAI-ORE|owl|reused|Europeana| -|http://bartoc.org/en/node/1822|Nomisma|Numismatic|CC BY 3.0|based on CIDOC-CRM, Dublin Core, SKOS und OAI-ORE|owl|reused|nomisma.org|consists of both an ontology and a terminology| -|http://bartoc.org/en/node/18274|SKOS|terminologies||RDF(S)|rdf|only indexed|| -|http://bartoc.org/en/node/857|BIBFRAME|bibliographies|Apache License 2.0||owl|reused||| -|http://bartoc.org/en/node/698|GNDO|GND|CC0 1.0||owl|reused||| -|http://bartoc.org/en/node/1674|GEONAMES|General: Geographic Names|CC BY 4.0||owl|reused|| -|http://bartoc.org/en/node/75|AAT|visual arts and architecture, cultural heritage|ODC-By 1.0|SKOS u.A.|skos|reused|| -|http://bartoc.org/en/node/430|GND||CC0 1.0|GNDO, SKOS, JSKOS|rdf|reused|| -||LADO|Archaeology|CC BY 4.0|based on CIDOC-CRM, Dublin Core, SKOS|owl|reused|https://archaeology.link| -|http://bartoc.org/en/node/94|CONA|cultural heritage, works regitration|(ODC-By) 1.0||||https://www.getty.edu/research/tools/vocabularies/cona/index.html| -|http://bartoc.org/en/node/109|TGN|geographic Names|(ODC-By) 1.0|JSON, RDF, N3/Turtle, N-Triples|skos|reused|https://www.getty.edu/research/tools/vocabularies/tgn/| -|http://bartoc.org/en/node/459|ICONCLASS|Ikonographie||FastAPI|skos|reused|https://iconclass.org/| -|none/multiple|IDAI.Vocab|Diverse Vokabulare Geo, Chronontology|https://idai.world/why/data-policy|several controlled vocabularies and thesauri|skos|reused|https://idai.world/how/thesauri-and-controlled-vocabularies| -|http://bartoc.org/en/node/505|Objektbezeichnungsdatei (OBG)|cultural heritage object naming|CC BY SA||rdf|reused|http://www.museumsvokabular.de/download/53/dd8b684e5595e22f5b94cc8476787095| +A collection of ontologies, controlled vocabularies, and schemas relevant for +the NFDI4Objects Consortium imported from the consortium's official BARTOC +record [https://bartoc.org/en/node/18961](https://bartoc.org/en/node/18961). + +Note: this collection is a subset of the BARTOC collection until all ontologies +and controlled vocabularies in the BARTOC collection are also curated in the +Semantic Farm. + +## Maintainers + +- [Jakob Voß](https://semantic.farm/orcid:0000-0002-7613-4123) +- [Anja Gerber](https://semantic.farm/orcid:0000-0003-2576-1511) +- [Florian Thiery](https://semantic.farm/orcid:0000-0002-3246-3531) +- [Kristina Fischer](https://semantic.farm/orcid:0009-0005-3991-1025) + +Suggest a new addition to this collection +[here](https://github.com/biopragmatics/bioregistry/issues/new?template=add-collection-prefix.yml&collection=0000036&title=Add%20prefix%20X%20to%20collection%200000036). + +## Ontologies + +The following table comes from Semantic Farm collection +[`0000036`](https://semantic.farm/collection/0000036), which is automatically +synced from the BARTOC collection +[`18961`](https://bartoc.org/vocabularies/?sort=relevance&order=desc&limit=10&filter=in%3Ahttp%3A%2F%2Fbartoc.org%2Fen%2Fnode%2F18961). + +| Prefix | Name | License | +| ---------------------------------------------------------------------------------- | --------------------------------------------------------------------------------- | ------------------------------------- | +| [`amh.material`](https://semantic.farm/amh.material) | Archäologisches Museum Hamburg – Stadtmuseum Harburg/Helms-Museum: Material terms | | +| [`bibo`](https://semantic.farm/bibo) | The Bibliographic Ontology | | +| [`bioregistry`](https://semantic.farm/bioregistry) | Bioregistry | CC0-1.0 | +| [`cidoc.crm`](https://semantic.farm/cidoc.crm) | CIDOC Conceptual Reference Model | | +| [`dai.thesauri`](https://semantic.farm/dai.thesauri) | German Archaeological Institute Thesaurus | CC-BY-4.0 | +| [`datacite.contributor`](https://semantic.farm/datacite.contributor) | DataCite Contributor Type | CC-BY-4.0 | +| [`datacite.date`](https://semantic.farm/datacite.date) | DataCite Date Type | CC-BY-4.0 | +| [`datacite.description`](https://semantic.farm/datacite.description) | DataCite Description Type | CC-BY-4.0 | +| [`datacite.identifier`](https://semantic.farm/datacite.identifier) | DataCite Related Identifier Type | CC-BY-4.0 | +| [`datacite.name`](https://semantic.farm/datacite.name) | DataCite Name Type | CC-BY-SA-4.0 | +| [`datacite.relation`](https://semantic.farm/datacite.relation) | DataCite Relation Type | CC-BY-4.0 | +| [`datacite.resource`](https://semantic.farm/datacite.resource) | DataCite Resource Type (General) | CC-BY-4.0 | +| [`fish.aoe`](https://semantic.farm/fish.aoe) | Forum on Information Standards in Heritage - Archaeological Objects Thesaurus | CC-BY-3.0 | +| [`fish.as`](https://semantic.farm/fish.as) | Forum on Information Standards in Heritage - Archaeological Sciences Thesaurus | CC-BY-3.0 | +| [`fish.bm`](https://semantic.farm/fish.bm) | Forum on Information Standards in Heritage - Building Materials Thesaurus | CC-BY-3.0 | +| [`fish.event`](https://semantic.farm/fish.event) | Forum on Information Standards in Heritage - Event Types Thesaurus | CC-BY-3.0 | +| [`fish.mc`](https://semantic.farm/fish.mc) | Forum on Information Standards in Heritage - Maritime Craft Types Thesaurus | CC-BY-3.0 | +| [`fish.mt`](https://semantic.farm/fish.mt) | Forum on Information Standards in Heritage - Thesaurus of Monument Types | CC-BY-3.0 | +| [`geonames`](https://semantic.farm/geonames) | GeoNames | CC-BY-4.0 | +| [`geosparql`](https://semantic.farm/geosparql) | GeoSPARQL | [Custom](https://www.ogc.org/license) | +| [`getty.att`](https://semantic.farm/getty.att) | Art and Architecture Thesaurus | ODC-By-1.0 | +| [`getty.tgn`](https://semantic.farm/getty.tgn) | Getty Thesaurus of Geographic Names | ODC-By-1.0 | +| [`getty.ulan`](https://semantic.farm/getty.ulan) | Union List of Artist Names | ODC-By-1.0 | +| [`gnd`](https://semantic.farm/gnd) | Gemeinsame Normdatei | CC0-1.0 | +| [`hessische.systematik`](https://semantic.farm/hessische.systematik) | Nomenclature for inventorying cultural history collections in museums | CC-BY-NC-SA-3.0 | +| [`iconclass`](https://semantic.farm/iconclass) | Iconclass Classification | ODbL-1.0 | +| [`kenom.material`](https://semantic.farm/kenom.material) | KENOM Material | | +| [`lado`](https://semantic.farm/lado) | Linked Archaeological Data Ontology | CC-BY-4.0 | +| [`lido.actor`](https://semantic.farm/lido.actor) | LIDO Terminology Actor Type | CC-BY-4.0 | +| [`lido.event`](https://semantic.farm/lido.event) | LIDO Terminology Event Type | CC-BY-4.0 | +| [`lido.identifier`](https://semantic.farm/lido.identifier) | LIDO Terminology Identifier Type | CC-BY-4.0 | +| [`lido.recordmetadatadate`](https://semantic.farm/lido.recordmetadatadate) | LIDO Terminology Record Metadata Date Type | CC-BY-SA-3.0 | +| [`lido.recordtype`](https://semantic.farm/lido.recordtype) | LIDO Terminology Record Type | CC-BY-4.0 | +| [`lido.repositoryset`](https://semantic.farm/lido.repositoryset) | LIDO Terminology Repository Set Type | CC-BY-4.0 | +| [`lido.resourcerepresentation`](https://semantic.farm/lido.resourcerepresentation) | LIDO Terminology Resource Representation Type | CC-BY-4.0 | +| [`lido.termmaterialstech`](https://semantic.farm/lido.termmaterialstech) | LIDO Terminology Term Materials Tech Type | CC-BY-4.0 | +| [`lv`](https://semantic.farm/lv) | lobid vocab | CC0-1.0 | +| [`oeai.ctp`](https://semantic.farm/oeai.ctp) | OeAI Thesaurus - Cultural Time Periods | CC-BY-4.0 | +| [`oeai.material`](https://semantic.farm/oeai.material) | OeAI Thesaurus - Materials | CC-BY-4.0 | +| [`orcid`](https://semantic.farm/orcid) | Open Researcher and Contributor | CC0-1.0 | +| [`ror`](https://semantic.farm/ror) | Research Organization Registry | CC0-1.0 | +| [`skos`](https://semantic.farm/skos) | Simple Knowledge Organization System | | +| [`time`](https://semantic.farm/time) | Time Ontology in OWL | CC-BY-4.0 | +| [`unesco.thesaurus`](https://semantic.farm/unesco.thesaurus) | UNESCO Thesaurus | CC-BY-3.0-IGO | +| [`viaf`](https://semantic.farm/viaf) | Virtual International Authority File | ODC-By-1.0 | +| [`whg`](https://semantic.farm/whg) | World Historical Gazetteer | CC-BY-NC-4.0 | +| [`wikidata`](https://semantic.farm/wikidata) | Wikidata | CC0-1.0 | + +## Colophon + +This page was automatically generated on 2026-05-07 using Semantic Farm +([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +by running the following commands: + +```console +$ git clone https://github.com/nfdi-de/nfdi-sections +$ cd nfdi-sections +$ uv run scripts/update_collections.py +$ git commit -am "Update WG Onto collections" +$ git push +``` diff --git a/docs/meta/wg_onto/used-ontologies/nfdixcs.md b/docs/meta/wg_onto/used-ontologies/nfdixcs.md index 8ba0cc4..aa5985c 100644 --- a/docs/meta/wg_onto/used-ontologies/nfdixcs.md +++ b/docs/meta/wg_onto/used-ontologies/nfdixcs.md @@ -2,7 +2,25 @@ title: NFDIxCS --- -Source: `/files/meta/Used_Ontologies_at_NFDI.xlsx` (sheet: NFDIxCS) +This consortia has not yet created an ontology list. -|Ontology ID|Domain|License|Modularity|Format|developed / reused / only indexed / only evaluated|Used in| -|---|---|---|---|---|---|---| +## Maintainers + +- [Fabian Huch](https://semantic.farm/orcid:0000-0002-9418-1580) + +Suggest a new addition to this collection +[here](https://github.com/biopragmatics/bioregistry/issues/new?template=add-collection-prefix.yml&collection=0000035&title=Add%20prefix%20X%20to%20collection%200000035). + +## Colophon + +This page was automatically generated on 2026-05-07 using Semantic Farm +([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +by running the following commands: + +```console +$ git clone https://github.com/nfdi-de/nfdi-sections +$ cd nfdi-sections +$ uv run scripts/update_collections.py +$ git commit -am "Update WG Onto collections" +$ git push +``` diff --git a/docs/meta/wg_onto/used-ontologies/punch4nfdi.md b/docs/meta/wg_onto/used-ontologies/punch4nfdi.md new file mode 100644 index 0000000..b23f336 --- /dev/null +++ b/docs/meta/wg_onto/used-ontologies/punch4nfdi.md @@ -0,0 +1,26 @@ +--- +title: PUNCH4NFDI +--- + +This consortia has not yet created an ontology list. + +## Maintainers + +- [Harry Enke](https://semantic.farm/orcid:0000-0002-2366-8316) + +Suggest a new addition to this collection +[here](https://github.com/biopragmatics/bioregistry/issues/new?template=add-collection-prefix.yml&collection=0000032&title=Add%20prefix%20X%20to%20collection%200000032). + +## Colophon + +This page was automatically generated on 2026-05-07 using Semantic Farm +([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +by running the following commands: + +```console +$ git clone https://github.com/nfdi-de/nfdi-sections +$ cd nfdi-sections +$ uv run scripts/update_collections.py +$ git commit -am "Update WG Onto collections" +$ git push +``` diff --git a/docs/meta/wg_onto/used-ontologies/text-plus.md b/docs/meta/wg_onto/used-ontologies/text-plus.md index a34cde5..15ba32e 100644 --- a/docs/meta/wg_onto/used-ontologies/text-plus.md +++ b/docs/meta/wg_onto/used-ontologies/text-plus.md @@ -2,29 +2,52 @@ title: Text+ --- -Source: `/files/meta/Used_Ontologies_at_NFDI.xlsx` (sheet: Text+) - -|BARTOC URI|Ontology ID|License|Domain|Format|Modularity|developed / reused / only indexed / only evaluated|Used in|Comments| -|---|---|---|---|---|---|---|---|---| -|none|LIDO|CC BY 4.0|Museum Sector, cultural heritage|xsd|based on CIDOC-CRM, CDWA, museumdat, and SPECTRUM|reused||| -|http://bartoc.org/en/node/20291|CIDOC-CRM|CC BY 4.0|Museum Sector, cultural heritage|owl|Abstract data model|reused||| -|http://bartoc.org/en/node/1576|CERIF|CC BY 3.0|Information about research (activities, institutions...)|owl||reused||| -|multiple|OntoME|CC BY 4.0||rdf|based on CIDOC-CRM|reused||| -|none (not one ontology)|TEI|CC BY 3.0|Textual Documents|xsd||reused||| -||MiMoText|CC0 1.0|Literary History (French Enlightenment Novel)|rdf|Wikibase-based, maps_to: "WIKIDATA, 11 modules"|reused|Mining and Modeling Text|| -|http://bartoc.org/en/node/20436|OntoLex|W3C Community FSA|Lexical resources|owl||reused||| -|http://bartoc.org/en/node/857|BIBFRAME|Apache License 2.0||owl||reused||| -|http://bartoc.org/en/node/963|CESSDA|CC BY-NC-SA 4.0||skos||reused||| -|http://bartoc.org/en/node/18706|DARIAH Backbone Thesaurus|||skos||reused||| -|http://bartoc.org/en/node/1674|GEONAMES|CC BY 4.0|General: Geographic Names|owl||reused||| -|https://bartoc.org/en/node/75|AAT|ODC-By 1.0|Culture: Art & Architecture|skos||reused||partOf Getty Vocabularies| -|https://bartoc.org/en/node/109|TGN|ODC-By 1.0|General: Geographic Names|skos||reused||partOf Getty Vocabularies| -|https://bartoc.org/en/node/94|CONA|ODC-By 1.0|Culture: Cultural Objects|skos||reused||partOf Getty Vocabularies| -|https://bartoc.org/en/node/118|ULAN|ODC-By 1.0|Culture: Artist Names & Information|skos||reused||partOf Getty Vocabularies| -|none|IA|ODC-By 1.0|Culture: proper names, relationships, and dates for iconographical narratives, religious or fictional characters, historical events, names of literary works and performing art|skos||reused||partOf Getty Vocabularies| -|https://bartoc.org/en/node/18498|CDWA|ODC-By 1.0|Culture: set of guidelines and cataloging rules for the description of art, architecture, and other cultural works|skos||reused||partOf Getty Vocabularies| -|http://bartoc.org/en/node/430|GND|CC0 1.0|General: authority file of named entities|rdf||reused||| -|http://bartoc.org/en/node/459|Iconclass||Art History|skos||reused||| -|multiple|Library of Congress Vocabularies||General: named entities|skos||reused||| -|multiple|Loterre vocabularies||General|skos||reused||| -|http://bartoc.org/en/node/18|Rameau||General|skos||reused||| +A placeholder collection of ontologies, controlled vocabularies, and schemas +relevant for the Text+ Consortium created by the +[NFDI Section Metadata WG Ontology Harmonization and Mapping](https://github.com/nfdi-de/section-metadata-wg-onto/). +The working group is in the process of identifying Text+ Consortium members +appropriate for maintaining this collection. + +## Maintainers + +- [Thorsten Trippel](https://semantic.farm/orcid:0000-0002-7211-7393) + +Suggest a new addition to this collection +[here](https://github.com/biopragmatics/bioregistry/issues/new?template=add-collection-prefix.yml&collection=0000038&title=Add%20prefix%20X%20to%20collection%200000038). + +## Ontologies + +The following table comes from Semantic Farm collection +[`0000038`](https://semantic.farm/collection/0000038). + +| Prefix | Name | License | +| -------------------------------------------------------------------------------- | --------------------------------------------------------- | ---------- | +| [`bibframe`](https://semantic.farm/bibframe) | Bibliographic Framework Initiative Vocabulary | CC0-1.0 | +| [`cessda.topicclassification`](https://semantic.farm/cessda.topicclassification) | CESSDA Topic Classification | CC-BY-4.0 | +| [`cidoc.crm`](https://semantic.farm/cidoc.crm) | CIDOC Conceptual Reference Model | | +| [`geonames`](https://semantic.farm/geonames) | GeoNames | CC-BY-4.0 | +| [`getty.att`](https://semantic.farm/getty.att) | Art and Architecture Thesaurus | ODC-By-1.0 | +| [`getty.cona`](https://semantic.farm/getty.cona) | Cultural Objects Names Authority | ODC-By-1.0 | +| [`getty.ia`](https://semantic.farm/getty.ia) | Getty Iconography Authority | | +| [`getty.tgn`](https://semantic.farm/getty.tgn) | Getty Thesaurus of Geographic Names | ODC-By-1.0 | +| [`getty.ulan`](https://semantic.farm/getty.ulan) | Union List of Artist Names | ODC-By-1.0 | +| [`gnd`](https://semantic.farm/gnd) | Gemeinsame Normdatei | CC0-1.0 | +| [`iconclass`](https://semantic.farm/iconclass) | Iconclass Classification | ODbL-1.0 | +| [`lido`](https://semantic.farm/lido) | Lightweight Information Describing Objects | CC-BY-4.0 | +| [`ontolex`](https://semantic.farm/ontolex) | Lexicon Model for Ontologies | | +| [`ontome`](https://semantic.farm/ontome) | Ontology Management Environment | CC-BY-4.0 | +| [`tadirah`](https://semantic.farm/tadirah) | Taxonomy of Digital Research Activities in the Humanities | CC0-1.0 | + +## Colophon + +This page was automatically generated on 2026-05-07 using Semantic Farm +([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +by running the following commands: + +```console +$ git clone https://github.com/nfdi-de/nfdi-sections +$ cd nfdi-sections +$ uv run scripts/update_collections.py +$ git commit -am "Update WG Onto collections" +$ git push +``` diff --git a/justfile b/justfile new file mode 100644 index 0000000..9b49b0e --- /dev/null +++ b/justfile @@ -0,0 +1,7 @@ +serve: + npm install + npm install @docusaurus/faster + npm start + +update-wg-onto: + uv run scripts/update_collections.py diff --git a/package-lock.json b/package-lock.json index 0de2683..54ac4a3 100644 --- a/package-lock.json +++ b/package-lock.json @@ -9,6 +9,7 @@ "version": "0.0.0", "dependencies": { "@docusaurus/core": "^3.9.1", + "@docusaurus/faster": "^3.10.1", "@docusaurus/preset-classic": "^3.9.1", "@mdx-js/react": "^3.0.0", "clsx": "^2.0.0", @@ -20,7 +21,8 @@ }, "devDependencies": { 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+ } + }, "node_modules/swr": { "version": "2.3.6", "resolved": "https://registry.npmjs.org/swr/-/swr-2.3.6.tgz", diff --git a/package.json b/package.json index 2554464..2442edf 100644 --- a/package.json +++ b/package.json @@ -15,6 +15,7 @@ }, "dependencies": { "@docusaurus/core": "^3.9.1", + "@docusaurus/faster": "^3.10.1", "@docusaurus/preset-classic": "^3.9.1", "@mdx-js/react": "^3.0.0", "clsx": "^2.0.0", @@ -26,7 +27,8 @@ }, "devDependencies": { "@docusaurus/module-type-aliases": "^3.9.1", - "@docusaurus/types": "^3.9.1" + "@docusaurus/types": "^3.9.1", + "baseline-browser-mapping": "^2.10.23" }, "browserslist": { "production": [ diff --git a/scripts/update_collections.py b/scripts/update_collections.py new file mode 100644 index 0000000..521c85d --- /dev/null +++ b/scripts/update_collections.py @@ -0,0 +1,212 @@ +# /// script +# requires-python = ">=3.14" +# dependencies = [ +# "bioregistry>=0.13.50", +# "click>=8.3.2", +# "tabulate>=0.10.0", +# ] +# /// + +"""Update collections.""" + +import datetime +import os +from pathlib import Path +from textwrap import dedent + +import bioregistry +import bioregistry.version +import click +from bioregistry.constants import NFDI_ROR +from tabulate import tabulate + +HERE = Path(__file__).parent.resolve() +ROOT = HERE.parent.resolve() +ONTOLOGIES = ROOT.joinpath("docs", "meta", "wg_onto", "used-ontologies").resolve() + +TODAY = datetime.date.today().strftime("%Y-%m-%d") +VERSION = bioregistry.version.get_version() +V_LINK = f"Semantic Farm ([v{VERSION}](https://github.com/biopragmatics/bioregistry/releases/tag/v{VERSION}))" + +RENAMES = {"text+": "text-plus", "berd@nfdi": "berd-nfdi"} +COLOPHON = f""" +## Colophon + +This page was automatically generated on {TODAY} using {V_LINK} by running the following commands: + +```console +$ git clone https://github.com/nfdi-de/nfdi-sections +$ cd nfdi-sections +$ uv run scripts/update_collections.py +$ git commit -am "Update WG Onto collections" +$ git push +``` +""" + + +@click.command() +def main() -> None: + for path in ONTOLOGIES.glob("*.md"): + path.unlink() + + index_rows = [] + for collection in bioregistry.read_collections().values(): + if not collection.has_organization_with_ror(NFDI_ROR): + continue + + name = collection.name.removesuffix(" Collection").strip() + path = get_collection_path(collection, name) + text = get_collection_text(collection, name) + path.write_text(text) + + index_rows.append( + ( + f"[{name}](/docs/meta/wg_onto/used-ontologies/{path.name})", + len(collection.resources) if collection_not_stub(collection) else "", + ", ".join(sorted(m.name for m in collection.maintainers or [])), + ) + ) + + index_text = dedent("""\ + --- + title: Used Ontologies + --- + + The NFDI Section Metadata Working Group on Ontology Harmonization and Mapping + has generated an overview of the ontologies, terminologies, controlled vocabularies, + and related semantic artifacts used by each consortium. + + We first partnered with members of each consortium to collaboratively construct their + respective collections in the [Semantic Farm](https://semantic.farm), a comprehensive + registry of ontologies, terminologies, controlled vocabularies, and related semantic + artifacts. These collections can be iteratively extended by following the "suggestion" + link on one of the following pages, by making + an issue on the Semantic Farm's issue tracker, or by editing the underlying + [single source of truth JSON file](https://github.com/biopragmatics/bioregistry/blob/main/src/bioregistry/data/collections.json). + + :::note + + Some consortia use external systems for curating their ontology lists. + For example, NFDI4Chem curates their collection directly in the TIB-TS, + NFDI4Biodiversity has their own OntoPortal instance for which all + loaded ontologies comprise their collection, and NFDI4Objects curates + their collection in BARTOC. In these cases, the collections are synced + into the Semantic Farm. Each consortia's collection page gives additional + context if it is maintained on an external system. + + ::: + + See source data at https://semantic.farm/collection/?ror=05qj6w324. + + ## Consortia + + """) + + index_text += "\n\n" + index_text += tabulate( + sorted(index_rows), + headers=["Consortium", "#", "Collection Maintainers"], + tablefmt="github", + ) + index_text += COLOPHON + + ONTOLOGIES.joinpath("index.md").write_text(index_text) + + os.system( + f"npx --yes prettier --check --prose-wrap always --write '{ONTOLOGIES}/*.md'" + ) + + +def collection_not_stub(collection: bioregistry.Collection) -> bool: + prefixes = set(collection.get_prefixes()) + return prefixes and prefixes != {"bioregistry"} + + +def get_collection_text(collection: bioregistry.Collection, name: str) -> str: + text = dedent(f"""\ + --- + title: {name} + --- + """) + + if collection_not_stub(collection): + text += collection.description + "\n" + else: + text += "This consortia has not yet created an ontology list.\n" + + if collection.maintainers: + text += "## Maintainers\n\n" + for maintainer in collection.maintainers: + text += f"- [{maintainer.name.strip()}](https://semantic.farm/orcid:{maintainer.orcid})\n" + text += "\n" + else: + text += "## Maintainers\n\nThis collection does not yet have maintainers.\n\n" + text += ( + f"\nSuggest a new addition to this collection [here](https://github.com/biopragmatics/bioregistry/" + f"issues/new?template=add-collection-prefix.yml&collection={collection.identifier}&title=Add%20prefix" + f"%20X%20to%20collection%20{collection.identifier}).\n\n" + ) + + rows = [] + + if collection_not_stub(collection): + has_comments = any( + annotation.comment for annotation in collection.get_annotated_prefixes() + ) + for annotation in collection.get_annotated_prefixes(): + resource = bioregistry.get_resource(annotation.prefix, strict=True) + + license = resource.get_license() + if license and license.startswith("http"): + license = f"[Custom]({license})" + + parts = [ + f"[`{resource.get_preferred_prefix() or resource.prefix}`](https://semantic.farm/{resource.prefix})", + resource.get_name(), + license, + ] + if has_comments: + parts.append(annotation.comment) + rows.append(tuple(parts)) + + headers = ["Prefix", "Name", "License"] + if has_comments: + headers.append("Comment") + text += dedent(f""" + ## Ontologies + + The following table comes from Semantic Farm collection + [`{collection.identifier}`](https://semantic.farm/collection/{collection.identifier}) + """).rstrip() + references = {r.prefix: r.identifier for r in collection.mappings or []} + if tib_collection := references.get("tib.collection"): + text += dedent(f"""\ + , which is automatically synced from the TIB Terminology Service + collection [`{tib_collection}`](https://service.tib.eu/terminology/collections/{tib_collection}). + """) + elif bartoc_collection := references.get("bartoc"): + text += dedent(f"""\ + , which is automatically synced from the BARTOC + collection [`{bartoc_collection}`](https://bartoc.org/vocabularies/?sort=relevance&order=desc&limit=10&filter=in%3Ahttp%3A%2F%2Fbartoc.org%2Fen%2Fnode%2F{bartoc_collection}). + """) + else: + text += "." + + text += "\n\n" + tabulate(rows, headers=headers, tablefmt="github") + "\n" + + # TODO add a "how to edit" section that either + # says to make a suggestion on Semantic Farm or to update + # upstream lists on TIB/BARTOC + + text += COLOPHON + return text + + +def get_collection_path(collection: bioregistry.Collection, name: str) -> Path: + key = RENAMES.get(name.lower(), name.lower()) + path = ONTOLOGIES.joinpath(key).with_suffix(".md") + return path + + +if __name__ == "__main__": + main() From 225301b39875c2abdd8834949813d2d58345aadf Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Thu, 7 May 2026 10:32:05 +0200 Subject: [PATCH 2/3] Fix typo --- docs/meta/wg_onto/used-ontologies/index.md | 2 +- docs/meta/wg_onto/used-ontologies/{ndfi4cat.md => nfdi4cat.md} | 0 scripts/update_collections.py | 2 +- 3 files changed, 2 insertions(+), 2 deletions(-) rename docs/meta/wg_onto/used-ontologies/{ndfi4cat.md => nfdi4cat.md} (100%) diff --git a/docs/meta/wg_onto/used-ontologies/index.md b/docs/meta/wg_onto/used-ontologies/index.md index c8bfe61..cb07766 100644 --- a/docs/meta/wg_onto/used-ontologies/index.md +++ b/docs/meta/wg_onto/used-ontologies/index.md @@ -40,7 +40,7 @@ See source data at https://semantic.farm/collection/?ror=05qj6w324. | [GHGA](/docs/meta/wg_onto/used-ontologies/ghga.md) | 12 | Karoline Mauer | | [KonsortSWD](/docs/meta/wg_onto/used-ontologies/konsortswd.md) | 37 | Noemi Betancort | | [MaRDI](/docs/meta/wg_onto/used-ontologies/mardi.md) | 8 | Björn Schembera | -| [NDFI4Cat](/docs/meta/wg_onto/used-ontologies/ndfi4cat.md) | 26 | Hendrik Borgelt, Alexander Behr, David Linke | +| [NDFI4Cat](/docs/meta/wg_onto/used-ontologies/nfdi4cat.md) | 26 | Hendrik Borgelt, Alexander Behr, David Linke | | [NFDI-MatWerk](/docs/meta/wg_onto/used-ontologies/nfdi-matwerk.md) | 6 | Ebrahim Nourouzi, Heike Fliegl | | [NFDI4BIOIMAGE](/docs/meta/wg_onto/used-ontologies/nfdi4bioimage.md) | 22 | Damien Goutte-Gattat | | [NFDI4Biodiversity](/docs/meta/wg_onto/used-ontologies/nfdi4biodiversity.md) | 65 | Naouel Karam, Ralph Schäfermeier | diff --git a/docs/meta/wg_onto/used-ontologies/ndfi4cat.md b/docs/meta/wg_onto/used-ontologies/nfdi4cat.md similarity index 100% rename from docs/meta/wg_onto/used-ontologies/ndfi4cat.md rename to docs/meta/wg_onto/used-ontologies/nfdi4cat.md diff --git a/scripts/update_collections.py b/scripts/update_collections.py index 521c85d..dae9434 100644 --- a/scripts/update_collections.py +++ b/scripts/update_collections.py @@ -28,7 +28,7 @@ VERSION = bioregistry.version.get_version() V_LINK = f"Semantic Farm ([v{VERSION}](https://github.com/biopragmatics/bioregistry/releases/tag/v{VERSION}))" -RENAMES = {"text+": "text-plus", "berd@nfdi": "berd-nfdi"} +RENAMES = {"text+": "text-plus", "berd@nfdi": "berd-nfdi", "ndfi4cat": "nfdi4cat"} COLOPHON = f""" ## Colophon From 382931627c0c1266a53d11c493b8b89cdbe0a032 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Fri, 8 May 2026 10:27:27 +0200 Subject: [PATCH 3/3] Update collections --- .../meta/wg_onto/used-ontologies/berd-nfdi.md | 4 +- .../wg_onto/used-ontologies/daphne4nfdi.md | 4 +- .../meta/wg_onto/used-ontologies/dataplant.md | 6 +- docs/meta/wg_onto/used-ontologies/fairagro.md | 4 +- docs/meta/wg_onto/used-ontologies/fairmat.md | 4 +- docs/meta/wg_onto/used-ontologies/ghga.md | 4 +- docs/meta/wg_onto/used-ontologies/index.md | 10 +- .../wg_onto/used-ontologies/konsortswd.md | 4 +- docs/meta/wg_onto/used-ontologies/mardi.md | 4 +- .../wg_onto/used-ontologies/nfdi-matwerk.md | 4 +- .../used-ontologies/nfdi4biodiversity.md | 6 +- .../wg_onto/used-ontologies/nfdi4bioimage.md | 6 +- docs/meta/wg_onto/used-ontologies/nfdi4cat.md | 6 +- .../meta/wg_onto/used-ontologies/nfdi4chem.md | 6 +- .../wg_onto/used-ontologies/nfdi4culture.md | 8 +- .../used-ontologies/nfdi4datascience.md | 4 +- .../wg_onto/used-ontologies/nfdi4earth.md | 6 +- .../wg_onto/used-ontologies/nfdi4energy.md | 4 +- .../wg_onto/used-ontologies/nfdi4health.md | 4 +- .../wg_onto/used-ontologies/nfdi4immuno.md | 4 +- docs/meta/wg_onto/used-ontologies/nfdi4ing.md | 9 +- .../wg_onto/used-ontologies/nfdi4memory.md | 4 +- .../used-ontologies/nfdi4microbiota.md | 4 +- .../wg_onto/used-ontologies/nfdi4objects.md | 102 +++++++++--------- docs/meta/wg_onto/used-ontologies/nfdixcs.md | 35 +++++- .../wg_onto/used-ontologies/punch4nfdi.md | 4 +- .../meta/wg_onto/used-ontologies/text-plus.md | 4 +- scripts/update_collections.py | 6 +- 28 files changed, 150 insertions(+), 120 deletions(-) diff --git a/docs/meta/wg_onto/used-ontologies/berd-nfdi.md b/docs/meta/wg_onto/used-ontologies/berd-nfdi.md index 20ebe1b..472c46b 100644 --- a/docs/meta/wg_onto/used-ontologies/berd-nfdi.md +++ b/docs/meta/wg_onto/used-ontologies/berd-nfdi.md @@ -29,8 +29,8 @@ The following table comes from Semantic Farm collection ## Colophon -This page was automatically generated on 2026-05-07 using Semantic Farm -([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +This page was automatically generated on 2026-05-08 using Semantic Farm +([v0.13.51](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.51)) by running the following commands: ```console diff --git a/docs/meta/wg_onto/used-ontologies/daphne4nfdi.md b/docs/meta/wg_onto/used-ontologies/daphne4nfdi.md index 61e9c37..18325f7 100644 --- a/docs/meta/wg_onto/used-ontologies/daphne4nfdi.md +++ b/docs/meta/wg_onto/used-ontologies/daphne4nfdi.md @@ -27,8 +27,8 @@ The following table comes from Semantic Farm collection ## Colophon -This page was automatically generated on 2026-05-07 using Semantic Farm -([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +This page was automatically generated on 2026-05-08 using Semantic Farm +([v0.13.51](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.51)) by running the following commands: ```console diff --git a/docs/meta/wg_onto/used-ontologies/dataplant.md b/docs/meta/wg_onto/used-ontologies/dataplant.md index 0536ec5..5b9c224 100644 --- a/docs/meta/wg_onto/used-ontologies/dataplant.md +++ b/docs/meta/wg_onto/used-ontologies/dataplant.md @@ -61,15 +61,15 @@ synced from the TIB Terminology Service collection | [`PSO`](https://semantic.farm/pso) | Plant Stress Ontology | CC-BY-4.0 | | [`RO`](https://semantic.farm/ro) | Relation Ontology | CC0-1.0 | | [`STATO`](https://semantic.farm/stato) | The Statistical Methods Ontology | CC-BY-3.0 | -| [`SWO`](https://semantic.farm/swo) | Software ontology | CC-BY-4.0 | +| [`SWO`](https://semantic.farm/swo) | Software Ontology | CC-BY-4.0 | | [`TO`](https://semantic.farm/to) | Plant Trait Ontology | CC-BY-4.0 | | [`UBERON`](https://semantic.farm/uberon) | Uber Anatomy Ontology | CC-BY-3.0 | | [`UO`](https://semantic.farm/uo) | Units of measurement ontology | CC-BY-3.0 | ## Colophon -This page was automatically generated on 2026-05-07 using Semantic Farm -([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +This page was automatically generated on 2026-05-08 using Semantic Farm +([v0.13.51](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.51)) by running the following commands: ```console diff --git a/docs/meta/wg_onto/used-ontologies/fairagro.md b/docs/meta/wg_onto/used-ontologies/fairagro.md index b1363be..a82d2a8 100644 --- a/docs/meta/wg_onto/used-ontologies/fairagro.md +++ b/docs/meta/wg_onto/used-ontologies/fairagro.md @@ -48,8 +48,8 @@ The following table comes from Semantic Farm collection ## Colophon -This page was automatically generated on 2026-05-07 using Semantic Farm -([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +This page was automatically generated on 2026-05-08 using Semantic Farm +([v0.13.51](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.51)) by running the following commands: ```console diff --git a/docs/meta/wg_onto/used-ontologies/fairmat.md b/docs/meta/wg_onto/used-ontologies/fairmat.md index 5dd2fff..f044bdf 100644 --- a/docs/meta/wg_onto/used-ontologies/fairmat.md +++ b/docs/meta/wg_onto/used-ontologies/fairmat.md @@ -33,8 +33,8 @@ synced from the TIB Terminology Service collection ## Colophon -This page was automatically generated on 2026-05-07 using Semantic Farm -([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +This page was automatically generated on 2026-05-08 using Semantic Farm +([v0.13.51](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.51)) by running the following commands: ```console diff --git a/docs/meta/wg_onto/used-ontologies/ghga.md b/docs/meta/wg_onto/used-ontologies/ghga.md index 5b82bda..7d2c884 100644 --- a/docs/meta/wg_onto/used-ontologies/ghga.md +++ b/docs/meta/wg_onto/used-ontologies/ghga.md @@ -37,8 +37,8 @@ The following table comes from Semantic Farm collection ## Colophon -This page was automatically generated on 2026-05-07 using Semantic Farm -([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +This page was automatically generated on 2026-05-08 using Semantic Farm +([v0.13.51](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.51)) by running the following commands: ```console diff --git a/docs/meta/wg_onto/used-ontologies/index.md b/docs/meta/wg_onto/used-ontologies/index.md index cb07766..21c7983 100644 --- a/docs/meta/wg_onto/used-ontologies/index.md +++ b/docs/meta/wg_onto/used-ontologies/index.md @@ -40,10 +40,10 @@ See source data at https://semantic.farm/collection/?ror=05qj6w324. | [GHGA](/docs/meta/wg_onto/used-ontologies/ghga.md) | 12 | Karoline Mauer | | [KonsortSWD](/docs/meta/wg_onto/used-ontologies/konsortswd.md) | 37 | Noemi Betancort | | [MaRDI](/docs/meta/wg_onto/used-ontologies/mardi.md) | 8 | Björn Schembera | -| [NDFI4Cat](/docs/meta/wg_onto/used-ontologies/nfdi4cat.md) | 26 | Hendrik Borgelt, Alexander Behr, David Linke | | [NFDI-MatWerk](/docs/meta/wg_onto/used-ontologies/nfdi-matwerk.md) | 6 | Ebrahim Nourouzi, Heike Fliegl | | [NFDI4BIOIMAGE](/docs/meta/wg_onto/used-ontologies/nfdi4bioimage.md) | 22 | Damien Goutte-Gattat | | [NFDI4Biodiversity](/docs/meta/wg_onto/used-ontologies/nfdi4biodiversity.md) | 65 | Naouel Karam, Ralph Schäfermeier | +| [NFDI4Cat](/docs/meta/wg_onto/used-ontologies/nfdi4cat.md) | 26 | Hendrik Borgelt, Alexander Behr, David Linke | | [NFDI4Chem](/docs/meta/wg_onto/used-ontologies/nfdi4chem.md) | 46 | Philip Strömert | | [NFDI4Culture](/docs/meta/wg_onto/used-ontologies/nfdi4culture.md) | 30 | Tabea Tietz | | [NFDI4DataScience](/docs/meta/wg_onto/used-ontologies/nfdi4datascience.md) | 3 | Benjamin Zapilko | @@ -51,18 +51,18 @@ See source data at https://semantic.farm/collection/?ror=05qj6w324. | [NFDI4Energy](/docs/meta/wg_onto/used-ontologies/nfdi4energy.md) | 17 | Amanda Wein | | [NFDI4Health](/docs/meta/wg_onto/used-ontologies/nfdi4health.md) | 38 | Matthias Löbe | | [NFDI4Immuno](/docs/meta/wg_onto/used-ontologies/nfdi4immuno.md) | | Sebastian Böhm, Ulrik Stervbo | -| [NFDI4Ing](/docs/meta/wg_onto/used-ontologies/nfdi4ing.md) | 102 | Dorothea Iglezakis, Giacomo Lanza, Susanne Arndt | +| [NFDI4Ing](/docs/meta/wg_onto/used-ontologies/nfdi4ing.md) | 103 | Dorothea Iglezakis, Giacomo Lanza, Susanne Arndt | | [NFDI4Memory](/docs/meta/wg_onto/used-ontologies/nfdi4memory.md) | 21 | Tabea Tietz | | [NFDI4Microbiota](/docs/meta/wg_onto/used-ontologies/nfdi4microbiota.md) | | Anandhi Iyappan, Maja Magel, Noriko Cassman | | [NFDI4Objects](/docs/meta/wg_onto/used-ontologies/nfdi4objects.md) | 47 | Anja Gerber, Florian Thiery, Jakob Voß, Kristina Fischer | -| [NFDIxCS](/docs/meta/wg_onto/used-ontologies/nfdixcs.md) | | Fabian Huch | +| [NFDIxCS](/docs/meta/wg_onto/used-ontologies/nfdixcs.md) | 18 | Fabian Huch | | [PUNCH4NFDI](/docs/meta/wg_onto/used-ontologies/punch4nfdi.md) | | Harry Enke | | [Text+](/docs/meta/wg_onto/used-ontologies/text-plus.md) | 15 | Thorsten Trippel | ## Colophon -This page was automatically generated on 2026-05-07 using Semantic Farm -([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +This page was automatically generated on 2026-05-08 using Semantic Farm +([v0.13.51](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.51)) by running the following commands: ```console diff --git a/docs/meta/wg_onto/used-ontologies/konsortswd.md b/docs/meta/wg_onto/used-ontologies/konsortswd.md index f0c8b92..9572eed 100644 --- a/docs/meta/wg_onto/used-ontologies/konsortswd.md +++ b/docs/meta/wg_onto/used-ontologies/konsortswd.md @@ -62,8 +62,8 @@ The following table comes from Semantic Farm collection ## Colophon -This page was automatically generated on 2026-05-07 using Semantic Farm -([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +This page was automatically generated on 2026-05-08 using Semantic Farm +([v0.13.51](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.51)) by running the following commands: ```console diff --git a/docs/meta/wg_onto/used-ontologies/mardi.md b/docs/meta/wg_onto/used-ontologies/mardi.md index de3ccc5..786117d 100644 --- a/docs/meta/wg_onto/used-ontologies/mardi.md +++ b/docs/meta/wg_onto/used-ontologies/mardi.md @@ -33,8 +33,8 @@ The following table comes from Semantic Farm collection ## Colophon -This page was automatically generated on 2026-05-07 using Semantic Farm -([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +This page was automatically generated on 2026-05-08 using Semantic Farm +([v0.13.51](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.51)) by running the following commands: ```console diff --git a/docs/meta/wg_onto/used-ontologies/nfdi-matwerk.md b/docs/meta/wg_onto/used-ontologies/nfdi-matwerk.md index 50fcc09..c2aeb28 100644 --- a/docs/meta/wg_onto/used-ontologies/nfdi-matwerk.md +++ b/docs/meta/wg_onto/used-ontologies/nfdi-matwerk.md @@ -30,8 +30,8 @@ The following table comes from Semantic Farm collection ## Colophon -This page was automatically generated on 2026-05-07 using Semantic Farm -([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +This page was automatically generated on 2026-05-08 using Semantic Farm +([v0.13.51](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.51)) by running the following commands: ```console diff --git a/docs/meta/wg_onto/used-ontologies/nfdi4biodiversity.md b/docs/meta/wg_onto/used-ontologies/nfdi4biodiversity.md index e418f32..0bf9fe7 100644 --- a/docs/meta/wg_onto/used-ontologies/nfdi4biodiversity.md +++ b/docs/meta/wg_onto/used-ontologies/nfdi4biodiversity.md @@ -79,7 +79,7 @@ The following table comes from Semantic Farm collection | [`sosa`](https://semantic.farm/sosa) | Sensor, Observation, Sample, and Actuator Ontology | [Custom](http://www.w3.org/Consortium/Legal/2015/copyright-software-and-document) | | [`sumso`](https://semantic.farm/sumso) | Sustainable Meat Systems Ontology | CC-BY-4.0 | | [`sweet`](https://semantic.farm/sweet) | Semantic Web for Earth and Environment Technology Ontology | CC0-1.0 | -| [`SWO`](https://semantic.farm/swo) | Software ontology | CC-BY-4.0 | +| [`SWO`](https://semantic.farm/swo) | Software Ontology | CC-BY-4.0 | | [`taxonconcept`](https://semantic.farm/taxonconcept) | TaxonConcept Ontology | | | [`TAXRANK`](https://semantic.farm/taxrank) | Taxonomic rank vocabulary | CC0-1.0 | | [`tib.bk`](https://semantic.farm/tib.bk) | Basic Classification | CC0-1.0 | @@ -91,8 +91,8 @@ The following table comes from Semantic Farm collection ## Colophon -This page was automatically generated on 2026-05-07 using Semantic Farm -([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +This page was automatically generated on 2026-05-08 using Semantic Farm +([v0.13.51](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.51)) by running the following commands: ```console diff --git a/docs/meta/wg_onto/used-ontologies/nfdi4bioimage.md b/docs/meta/wg_onto/used-ontologies/nfdi4bioimage.md index 41479b9..8c91853 100644 --- a/docs/meta/wg_onto/used-ontologies/nfdi4bioimage.md +++ b/docs/meta/wg_onto/used-ontologies/nfdi4bioimage.md @@ -38,14 +38,14 @@ The following table comes from Semantic Farm collection | [`OBI`](https://semantic.farm/obi) | Ontology for Biomedical Investigations | CC-BY-4.0 | | [`radlex`](https://semantic.farm/radlex) | RSNA Informatics RadLex | [Custom](http://www.rsna.org/uploadedFiles/RSNA/Content/Informatics/RadLex_License_Agreement_and_Terms_of_Use_V2_Final.pdf) | | [`snomedct`](https://semantic.farm/snomedct) | SNOMED CT (International Edition) | [Custom](https://uts.nlm.nih.gov/uts/assets/LicenseAgreement.pdf) | -| [`SWO`](https://semantic.farm/swo) | Software ontology | CC-BY-4.0 | +| [`SWO`](https://semantic.farm/swo) | Software Ontology | CC-BY-4.0 | | [`UBERON`](https://semantic.farm/uberon) | Uber Anatomy Ontology | CC-BY-3.0 | | [`UO`](https://semantic.farm/uo) | Units of measurement ontology | CC-BY-3.0 | ## Colophon -This page was automatically generated on 2026-05-07 using Semantic Farm -([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +This page was automatically generated on 2026-05-08 using Semantic Farm +([v0.13.51](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.51)) by running the following commands: ```console diff --git a/docs/meta/wg_onto/used-ontologies/nfdi4cat.md b/docs/meta/wg_onto/used-ontologies/nfdi4cat.md index 367711a..506d88a 100644 --- a/docs/meta/wg_onto/used-ontologies/nfdi4cat.md +++ b/docs/meta/wg_onto/used-ontologies/nfdi4cat.md @@ -1,5 +1,5 @@ --- -title: NDFI4Cat +title: NFDI4Cat --- A collection of ontologies, controlled vocabularies, and schemas relevant for @@ -61,8 +61,8 @@ synced from the TIB Terminology Service collection ## Colophon -This page was automatically generated on 2026-05-07 using Semantic Farm -([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +This page was automatically generated on 2026-05-08 using Semantic Farm +([v0.13.51](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.51)) by running the following commands: ```console diff --git a/docs/meta/wg_onto/used-ontologies/nfdi4chem.md b/docs/meta/wg_onto/used-ontologies/nfdi4chem.md index 4b2f084..d65b568 100644 --- a/docs/meta/wg_onto/used-ontologies/nfdi4chem.md +++ b/docs/meta/wg_onto/used-ontologies/nfdi4chem.md @@ -69,7 +69,7 @@ synced from the TIB Terminology Service collection | [`sosa`](https://semantic.farm/sosa) | Sensor, Observation, Sample, and Actuator Ontology | [Custom](http://www.w3.org/Consortium/Legal/2015/copyright-software-and-document) | | | [`ssn`](https://semantic.farm/ssn) | Semantic Sensor Network Ontology | [Custom](http://www.w3.org/Consortium/Legal/2015/copyright-software-and-document) | | | [`ssn.system`](https://semantic.farm/ssn.system) | System capabilities, operating ranges, and survival ranges ontology | [Custom](http://www.w3.org/Consortium/Legal/2015/copyright-software-and-document) | | -| [`SWO`](https://semantic.farm/swo) | Software ontology | CC-BY-4.0 | | +| [`SWO`](https://semantic.farm/swo) | Software Ontology | CC-BY-4.0 | | | [`time`](https://semantic.farm/time) | Time Ontology in OWL | CC-BY-4.0 | | | [`UO`](https://semantic.farm/uo) | Units of measurement ontology | CC-BY-3.0 | | | [`vibso`](https://semantic.farm/vibso) | Vibrational Spectroscopy Ontology | CC-BY-4.0 | | @@ -80,8 +80,8 @@ synced from the TIB Terminology Service collection ## Colophon -This page was automatically generated on 2026-05-07 using Semantic Farm -([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +This page was automatically generated on 2026-05-08 using Semantic Farm +([v0.13.51](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.51)) by running the following commands: ```console diff --git a/docs/meta/wg_onto/used-ontologies/nfdi4culture.md b/docs/meta/wg_onto/used-ontologies/nfdi4culture.md index 49cd458..590785d 100644 --- a/docs/meta/wg_onto/used-ontologies/nfdi4culture.md +++ b/docs/meta/wg_onto/used-ontologies/nfdi4culture.md @@ -32,7 +32,7 @@ synced from the TIB Terminology Service collection | [`dbo`](https://semantic.farm/dbo) | DBPedia Ontology | | | [`dcat`](https://semantic.farm/dcat) | Data Catalog | CC-BY-4.0 | | [`dcterms`](https://semantic.farm/dcterms) | Dublin Core Metadata Initiative Terms | | -| [`doap`](https://semantic.farm/doap) | Description of a Project | | +| [`doap`](https://semantic.farm/doap) | Description of a Project | Apache-2.0 | | [`fabio`](https://semantic.farm/fabio) | FaBiO, the FRBR-aligned Bibliographic Ontology | CC-BY-4.0 | | [`foaf`](https://semantic.farm/foaf) | Friend of a Friend | CC-BY-1.0 | | [`FRAPO`](https://semantic.farm/frapo) | Funding, Research Administration and Projects Ontology | | @@ -51,7 +51,7 @@ synced from the TIB Terminology Service collection | [`premis`](https://semantic.farm/premis) | PREMIS 3 Ontology | | | [`schema`](https://semantic.farm/schema) | Schema.org | | | [`skos`](https://semantic.farm/skos) | Simple Knowledge Organization System | | -| [`SWO`](https://semantic.farm/swo) | Software ontology | CC-BY-4.0 | +| [`SWO`](https://semantic.farm/swo) | Software Ontology | CC-BY-4.0 | | [`vcard`](https://semantic.farm/vcard) | Virtual Contact File | | | [`viaf`](https://semantic.farm/viaf) | Virtual International Authority File | ODC-By-1.0 | | [`vivo`](https://semantic.farm/vivo) | VIVO Ontology | Unlicense | @@ -59,8 +59,8 @@ synced from the TIB Terminology Service collection ## Colophon -This page was automatically generated on 2026-05-07 using Semantic Farm -([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +This page was automatically generated on 2026-05-08 using Semantic Farm +([v0.13.51](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.51)) by running the following commands: ```console diff --git a/docs/meta/wg_onto/used-ontologies/nfdi4datascience.md b/docs/meta/wg_onto/used-ontologies/nfdi4datascience.md index 6a929da..e9b97ad 100644 --- a/docs/meta/wg_onto/used-ontologies/nfdi4datascience.md +++ b/docs/meta/wg_onto/used-ontologies/nfdi4datascience.md @@ -28,8 +28,8 @@ The following table comes from Semantic Farm collection ## Colophon -This page was automatically generated on 2026-05-07 using Semantic Farm -([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +This page was automatically generated on 2026-05-08 using Semantic Farm +([v0.13.51](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.51)) by running the following commands: ```console diff --git a/docs/meta/wg_onto/used-ontologies/nfdi4earth.md b/docs/meta/wg_onto/used-ontologies/nfdi4earth.md index 358ae92..cbbbacc 100644 --- a/docs/meta/wg_onto/used-ontologies/nfdi4earth.md +++ b/docs/meta/wg_onto/used-ontologies/nfdi4earth.md @@ -31,7 +31,7 @@ The following table comes from Semantic Farm collection | [`foaf`](https://semantic.farm/foaf) | Friend of a Friend | CC-BY-1.0 | | [`GAZ`](https://semantic.farm/gaz) | Gazetteer | CC0-1.0 | | [`geonames`](https://semantic.farm/geonames) | GeoNames | CC-BY-4.0 | -| [`geosparql`](https://semantic.farm/geosparql) | GeoSPARQL | [Custom](https://www.ogc.org/license) | +| [`geosparql`](https://semantic.farm/geosparql) | GeoSPARQL | [Custom](http://purl.org/NET/rdflicense/:APACHE2.0) | | [`legacy.ao`](https://semantic.farm/legacy.ao) | Annotation Ontology | CC-BY-3.0 | | [`n4e`](https://semantic.farm/n4e) | NFDI4Earth Ontology | CC0-1.0 | | [`NCBITaxon`](https://semantic.farm/ncbitaxon) | NCBI Taxonomy | CC0-1.0 | @@ -52,8 +52,8 @@ The following table comes from Semantic Farm collection ## Colophon -This page was automatically generated on 2026-05-07 using Semantic Farm -([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +This page was automatically generated on 2026-05-08 using Semantic Farm +([v0.13.51](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.51)) by running the following commands: ```console diff --git a/docs/meta/wg_onto/used-ontologies/nfdi4energy.md b/docs/meta/wg_onto/used-ontologies/nfdi4energy.md index 8cb7c7a..aa424c9 100644 --- a/docs/meta/wg_onto/used-ontologies/nfdi4energy.md +++ b/docs/meta/wg_onto/used-ontologies/nfdi4energy.md @@ -40,8 +40,8 @@ synced from the TIB Terminology Service collection ## Colophon -This page was automatically generated on 2026-05-07 using Semantic Farm -([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +This page was automatically generated on 2026-05-08 using Semantic Farm +([v0.13.51](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.51)) by running the following commands: ```console diff --git a/docs/meta/wg_onto/used-ontologies/nfdi4health.md b/docs/meta/wg_onto/used-ontologies/nfdi4health.md index ed8bcd3..5d3c6f0 100644 --- a/docs/meta/wg_onto/used-ontologies/nfdi4health.md +++ b/docs/meta/wg_onto/used-ontologies/nfdi4health.md @@ -63,8 +63,8 @@ The following table comes from Semantic Farm collection ## Colophon -This page was automatically generated on 2026-05-07 using Semantic Farm -([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +This page was automatically generated on 2026-05-08 using Semantic Farm +([v0.13.51](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.51)) by running the following commands: ```console diff --git a/docs/meta/wg_onto/used-ontologies/nfdi4immuno.md b/docs/meta/wg_onto/used-ontologies/nfdi4immuno.md index f6490ec..5371c5d 100644 --- a/docs/meta/wg_onto/used-ontologies/nfdi4immuno.md +++ b/docs/meta/wg_onto/used-ontologies/nfdi4immuno.md @@ -14,8 +14,8 @@ Suggest a new addition to this collection ## Colophon -This page was automatically generated on 2026-05-07 using Semantic Farm -([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +This page was automatically generated on 2026-05-08 using Semantic Farm +([v0.13.51](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.51)) by running the following commands: ```console diff --git a/docs/meta/wg_onto/used-ontologies/nfdi4ing.md b/docs/meta/wg_onto/used-ontologies/nfdi4ing.md index 168650b..90a18a8 100644 --- a/docs/meta/wg_onto/used-ontologies/nfdi4ing.md +++ b/docs/meta/wg_onto/used-ontologies/nfdi4ing.md @@ -55,7 +55,7 @@ synced from the TIB Terminology Service collection | [`findex.bau`](https://semantic.farm/findex.bau) | FINDEX Bau as a SKOS Thesaurus - Facetted Indexing System for Civil Engineering | | | [`findex.raum`](https://semantic.farm/findex.raum) | FINDEX Raum | | | [`ftonto`](https://semantic.farm/ftonto) | Fischertechnik Ontology | | -| [`geosparql`](https://semantic.farm/geosparql) | GeoSPARQL | [Custom](https://www.ogc.org/license) | +| [`geosparql`](https://semantic.farm/geosparql) | GeoSPARQL | [Custom](http://purl.org/NET/rdflicense/:APACHE2.0) | | [`gist`](https://semantic.farm/gist) | gist | CC-BY-4.0 | | [`IAO`](https://semantic.farm/iao) | Information Artifact Ontology | CC-BY-4.0 | | [`idsa`](https://semantic.farm/idsa) | International Data Spaces Information Model | | @@ -72,6 +72,7 @@ synced from the TIB Terminology Service collection | [`mathmoddb`](https://semantic.farm/mathmoddb) | MathModDB Ontology and Knowledge Graph for Mathematical Models | CC-BY-4.0 | | [`mobivoc`](https://semantic.farm/mobivoc) | MobiVoc Open Mobility Vocabulary 1.1.4 | | | [`modsci`](https://semantic.farm/modsci) | Modern Science Ontology | | +| [`mwo`](https://semantic.farm/mwo) | NFDI MatWerk Ontology | CC0-1.0 | | [`OEO`](https://semantic.farm/oeo) | Open Energy Ontology | CC0-1.0 | | [`okn.sd`](https://semantic.farm/okn.sd) | The Software Description Ontology | | | [`om`](https://semantic.farm/om) | Ontology of units of Measure | CC-BY-4.0 | @@ -101,7 +102,7 @@ synced from the TIB Terminology Service collection | [`ssn`](https://semantic.farm/ssn) | Semantic Sensor Network Ontology | [Custom](http://www.w3.org/Consortium/Legal/2015/copyright-software-and-document) | | [`ssn.system`](https://semantic.farm/ssn.system) | System capabilities, operating ranges, and survival ranges ontology | [Custom](http://www.w3.org/Consortium/Legal/2015/copyright-software-and-document) | | [`sweet`](https://semantic.farm/sweet) | Semantic Web for Earth and Environment Technology Ontology | CC0-1.0 | -| [`SWO`](https://semantic.farm/swo) | Software ontology | CC-BY-4.0 | +| [`SWO`](https://semantic.farm/swo) | Software Ontology | CC-BY-4.0 | | [`T4FS`](https://semantic.farm/t4fs) | terms4FAIRskills | CC-BY-4.0 | | [`tib.bk`](https://semantic.farm/tib.bk) | Basic Classification | CC0-1.0 | | [`tib.bo`](https://semantic.farm/tib.bo) | Base Ontology | | @@ -130,8 +131,8 @@ synced from the TIB Terminology Service collection ## Colophon -This page was automatically generated on 2026-05-07 using Semantic Farm -([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +This page was automatically generated on 2026-05-08 using Semantic Farm +([v0.13.51](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.51)) by running the following commands: ```console diff --git a/docs/meta/wg_onto/used-ontologies/nfdi4memory.md b/docs/meta/wg_onto/used-ontologies/nfdi4memory.md index c5665ae..6db2aa3 100644 --- a/docs/meta/wg_onto/used-ontologies/nfdi4memory.md +++ b/docs/meta/wg_onto/used-ontologies/nfdi4memory.md @@ -46,8 +46,8 @@ The following table comes from Semantic Farm collection ## Colophon -This page was automatically generated on 2026-05-07 using Semantic Farm -([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +This page was automatically generated on 2026-05-08 using Semantic Farm +([v0.13.51](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.51)) by running the following commands: ```console diff --git a/docs/meta/wg_onto/used-ontologies/nfdi4microbiota.md b/docs/meta/wg_onto/used-ontologies/nfdi4microbiota.md index 375162c..6f991e5 100644 --- a/docs/meta/wg_onto/used-ontologies/nfdi4microbiota.md +++ b/docs/meta/wg_onto/used-ontologies/nfdi4microbiota.md @@ -15,8 +15,8 @@ Suggest a new addition to this collection ## Colophon -This page was automatically generated on 2026-05-07 using Semantic Farm -([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +This page was automatically generated on 2026-05-08 using Semantic Farm +([v0.13.51](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.51)) by running the following commands: ```console diff --git a/docs/meta/wg_onto/used-ontologies/nfdi4objects.md b/docs/meta/wg_onto/used-ontologies/nfdi4objects.md index 7066696..e3b978f 100644 --- a/docs/meta/wg_onto/used-ontologies/nfdi4objects.md +++ b/docs/meta/wg_onto/used-ontologies/nfdi4objects.md @@ -27,60 +27,60 @@ The following table comes from Semantic Farm collection synced from the BARTOC collection [`18961`](https://bartoc.org/vocabularies/?sort=relevance&order=desc&limit=10&filter=in%3Ahttp%3A%2F%2Fbartoc.org%2Fen%2Fnode%2F18961). -| Prefix | Name | License | -| ---------------------------------------------------------------------------------- | --------------------------------------------------------------------------------- | ------------------------------------- | -| [`amh.material`](https://semantic.farm/amh.material) | Archäologisches Museum Hamburg – Stadtmuseum Harburg/Helms-Museum: Material terms | | -| [`bibo`](https://semantic.farm/bibo) | The Bibliographic Ontology | | -| [`bioregistry`](https://semantic.farm/bioregistry) | Bioregistry | CC0-1.0 | -| [`cidoc.crm`](https://semantic.farm/cidoc.crm) | CIDOC Conceptual Reference Model | | -| [`dai.thesauri`](https://semantic.farm/dai.thesauri) | German Archaeological Institute Thesaurus | CC-BY-4.0 | -| [`datacite.contributor`](https://semantic.farm/datacite.contributor) | DataCite Contributor Type | CC-BY-4.0 | -| [`datacite.date`](https://semantic.farm/datacite.date) | DataCite Date Type | CC-BY-4.0 | -| [`datacite.description`](https://semantic.farm/datacite.description) | DataCite Description Type | CC-BY-4.0 | -| [`datacite.identifier`](https://semantic.farm/datacite.identifier) | DataCite Related Identifier Type | CC-BY-4.0 | -| [`datacite.name`](https://semantic.farm/datacite.name) | DataCite Name Type | CC-BY-SA-4.0 | -| [`datacite.relation`](https://semantic.farm/datacite.relation) | DataCite Relation Type | CC-BY-4.0 | -| [`datacite.resource`](https://semantic.farm/datacite.resource) | DataCite Resource Type (General) | CC-BY-4.0 | -| [`fish.aoe`](https://semantic.farm/fish.aoe) | Forum on Information Standards in Heritage - Archaeological Objects Thesaurus | CC-BY-3.0 | -| [`fish.as`](https://semantic.farm/fish.as) | Forum on Information Standards in Heritage - Archaeological Sciences Thesaurus | CC-BY-3.0 | -| [`fish.bm`](https://semantic.farm/fish.bm) | Forum on Information Standards in Heritage - Building Materials Thesaurus | CC-BY-3.0 | -| [`fish.event`](https://semantic.farm/fish.event) | Forum on Information Standards in Heritage - Event Types Thesaurus | CC-BY-3.0 | -| [`fish.mc`](https://semantic.farm/fish.mc) | Forum on Information Standards in Heritage - Maritime Craft Types Thesaurus | CC-BY-3.0 | -| [`fish.mt`](https://semantic.farm/fish.mt) | Forum on Information Standards in Heritage - Thesaurus of Monument Types | CC-BY-3.0 | -| [`geonames`](https://semantic.farm/geonames) | GeoNames | CC-BY-4.0 | -| [`geosparql`](https://semantic.farm/geosparql) | GeoSPARQL | [Custom](https://www.ogc.org/license) | -| [`getty.att`](https://semantic.farm/getty.att) | Art and Architecture Thesaurus | ODC-By-1.0 | -| [`getty.tgn`](https://semantic.farm/getty.tgn) | Getty Thesaurus of Geographic Names | ODC-By-1.0 | -| [`getty.ulan`](https://semantic.farm/getty.ulan) | Union List of Artist Names | ODC-By-1.0 | -| [`gnd`](https://semantic.farm/gnd) | Gemeinsame Normdatei | CC0-1.0 | -| [`hessische.systematik`](https://semantic.farm/hessische.systematik) | Nomenclature for inventorying cultural history collections in museums | CC-BY-NC-SA-3.0 | -| [`iconclass`](https://semantic.farm/iconclass) | Iconclass Classification | ODbL-1.0 | -| [`kenom.material`](https://semantic.farm/kenom.material) | KENOM Material | | -| [`lado`](https://semantic.farm/lado) | Linked Archaeological Data Ontology | CC-BY-4.0 | -| [`lido.actor`](https://semantic.farm/lido.actor) | LIDO Terminology Actor Type | CC-BY-4.0 | -| [`lido.event`](https://semantic.farm/lido.event) | LIDO Terminology Event Type | CC-BY-4.0 | -| [`lido.identifier`](https://semantic.farm/lido.identifier) | LIDO Terminology Identifier Type | CC-BY-4.0 | -| [`lido.recordmetadatadate`](https://semantic.farm/lido.recordmetadatadate) | LIDO Terminology Record Metadata Date Type | CC-BY-SA-3.0 | -| [`lido.recordtype`](https://semantic.farm/lido.recordtype) | LIDO Terminology Record Type | CC-BY-4.0 | -| [`lido.repositoryset`](https://semantic.farm/lido.repositoryset) | LIDO Terminology Repository Set Type | CC-BY-4.0 | -| [`lido.resourcerepresentation`](https://semantic.farm/lido.resourcerepresentation) | LIDO Terminology Resource Representation Type | CC-BY-4.0 | -| [`lido.termmaterialstech`](https://semantic.farm/lido.termmaterialstech) | LIDO Terminology Term Materials Tech Type | CC-BY-4.0 | -| [`lv`](https://semantic.farm/lv) | lobid vocab | CC0-1.0 | -| [`oeai.ctp`](https://semantic.farm/oeai.ctp) | OeAI Thesaurus - Cultural Time Periods | CC-BY-4.0 | -| [`oeai.material`](https://semantic.farm/oeai.material) | OeAI Thesaurus - Materials | CC-BY-4.0 | -| [`orcid`](https://semantic.farm/orcid) | Open Researcher and Contributor | CC0-1.0 | -| [`ror`](https://semantic.farm/ror) | Research Organization Registry | CC0-1.0 | -| [`skos`](https://semantic.farm/skos) | Simple Knowledge Organization System | | -| [`time`](https://semantic.farm/time) | Time Ontology in OWL | CC-BY-4.0 | -| [`unesco.thesaurus`](https://semantic.farm/unesco.thesaurus) | UNESCO Thesaurus | CC-BY-3.0-IGO | -| [`viaf`](https://semantic.farm/viaf) | Virtual International Authority File | ODC-By-1.0 | -| [`whg`](https://semantic.farm/whg) | World Historical Gazetteer | CC-BY-NC-4.0 | -| [`wikidata`](https://semantic.farm/wikidata) | Wikidata | CC0-1.0 | +| Prefix | Name | License | +| ---------------------------------------------------------------------------------- | --------------------------------------------------------------------------------- | --------------------------------------------------- | +| [`amh.material`](https://semantic.farm/amh.material) | Archäologisches Museum Hamburg – Stadtmuseum Harburg/Helms-Museum: Material terms | | +| [`bibo`](https://semantic.farm/bibo) | The Bibliographic Ontology | | +| [`bioregistry`](https://semantic.farm/bioregistry) | Bioregistry | CC0-1.0 | +| [`cidoc.crm`](https://semantic.farm/cidoc.crm) | CIDOC Conceptual Reference Model | | +| [`dai.thesauri`](https://semantic.farm/dai.thesauri) | German Archaeological Institute Thesaurus | CC-BY-4.0 | +| [`datacite.contributor`](https://semantic.farm/datacite.contributor) | DataCite Contributor Type | CC-BY-4.0 | +| [`datacite.date`](https://semantic.farm/datacite.date) | DataCite Date Type | CC-BY-4.0 | +| [`datacite.description`](https://semantic.farm/datacite.description) | DataCite Description Type | CC-BY-4.0 | +| [`datacite.identifier`](https://semantic.farm/datacite.identifier) | DataCite Related Identifier Type | CC-BY-4.0 | +| [`datacite.name`](https://semantic.farm/datacite.name) | DataCite Name Type | CC-BY-SA-4.0 | +| [`datacite.relation`](https://semantic.farm/datacite.relation) | DataCite Relation Type | CC-BY-4.0 | +| [`datacite.resource`](https://semantic.farm/datacite.resource) | DataCite Resource Type (General) | CC-BY-4.0 | +| [`fish.aoe`](https://semantic.farm/fish.aoe) | Forum on Information Standards in Heritage - Archaeological Objects Thesaurus | CC-BY-3.0 | +| [`fish.as`](https://semantic.farm/fish.as) | Forum on Information Standards in Heritage - Archaeological Sciences Thesaurus | CC-BY-3.0 | +| [`fish.bm`](https://semantic.farm/fish.bm) | Forum on Information Standards in Heritage - Building Materials Thesaurus | CC-BY-3.0 | +| [`fish.event`](https://semantic.farm/fish.event) | Forum on Information Standards in Heritage - Event Types Thesaurus | CC-BY-3.0 | +| [`fish.mc`](https://semantic.farm/fish.mc) | Forum on Information Standards in Heritage - Maritime Craft Types Thesaurus | CC-BY-3.0 | +| [`fish.mt`](https://semantic.farm/fish.mt) | Forum on Information Standards in Heritage - Thesaurus of Monument Types | CC-BY-3.0 | +| [`geonames`](https://semantic.farm/geonames) | GeoNames | CC-BY-4.0 | +| [`geosparql`](https://semantic.farm/geosparql) | GeoSPARQL | [Custom](http://purl.org/NET/rdflicense/:APACHE2.0) | +| [`getty.att`](https://semantic.farm/getty.att) | Art and Architecture Thesaurus | ODC-By-1.0 | +| [`getty.tgn`](https://semantic.farm/getty.tgn) | Getty Thesaurus of Geographic Names | ODC-By-1.0 | +| [`getty.ulan`](https://semantic.farm/getty.ulan) | Union List of Artist Names | ODC-By-1.0 | +| [`gnd`](https://semantic.farm/gnd) | Gemeinsame Normdatei | CC0-1.0 | +| [`hessische.systematik`](https://semantic.farm/hessische.systematik) | Nomenclature for inventorying cultural history collections in museums | CC-BY-NC-SA-3.0 | +| [`iconclass`](https://semantic.farm/iconclass) | Iconclass Classification | ODbL-1.0 | +| [`kenom.material`](https://semantic.farm/kenom.material) | KENOM Material | | +| [`lado`](https://semantic.farm/lado) | Linked Archaeological Data Ontology | CC-BY-4.0 | +| [`lido.actor`](https://semantic.farm/lido.actor) | LIDO Terminology Actor Type | CC-BY-4.0 | +| [`lido.event`](https://semantic.farm/lido.event) | LIDO Terminology Event Type | CC-BY-4.0 | +| [`lido.identifier`](https://semantic.farm/lido.identifier) | LIDO Terminology Identifier Type | CC-BY-4.0 | +| [`lido.recordmetadatadate`](https://semantic.farm/lido.recordmetadatadate) | LIDO Terminology Record Metadata Date Type | CC-BY-SA-3.0 | +| [`lido.recordtype`](https://semantic.farm/lido.recordtype) | LIDO Terminology Record Type | CC-BY-4.0 | +| [`lido.repositoryset`](https://semantic.farm/lido.repositoryset) | LIDO Terminology Repository Set Type | CC-BY-4.0 | +| [`lido.resourcerepresentation`](https://semantic.farm/lido.resourcerepresentation) | LIDO Terminology Resource Representation Type | CC-BY-4.0 | +| [`lido.termmaterialstech`](https://semantic.farm/lido.termmaterialstech) | LIDO Terminology Term Materials Tech Type | CC-BY-4.0 | +| [`lv`](https://semantic.farm/lv) | lobid vocab | CC0-1.0 | +| [`oeai.ctp`](https://semantic.farm/oeai.ctp) | OeAI Thesaurus - Cultural Time Periods | CC-BY-4.0 | +| [`oeai.material`](https://semantic.farm/oeai.material) | OeAI Thesaurus - Materials | CC-BY-4.0 | +| [`orcid`](https://semantic.farm/orcid) | Open Researcher and Contributor | CC0-1.0 | +| [`ror`](https://semantic.farm/ror) | Research Organization Registry | CC0-1.0 | +| [`skos`](https://semantic.farm/skos) | Simple Knowledge Organization System | | +| [`time`](https://semantic.farm/time) | Time Ontology in OWL | CC-BY-4.0 | +| [`unesco.thesaurus`](https://semantic.farm/unesco.thesaurus) | UNESCO Thesaurus | CC-BY-3.0-IGO | +| [`viaf`](https://semantic.farm/viaf) | Virtual International Authority File | ODC-By-1.0 | +| [`whg`](https://semantic.farm/whg) | World Historical Gazetteer | CC-BY-NC-4.0 | +| [`wikidata`](https://semantic.farm/wikidata) | Wikidata | CC0-1.0 | ## Colophon -This page was automatically generated on 2026-05-07 using Semantic Farm -([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +This page was automatically generated on 2026-05-08 using Semantic Farm +([v0.13.51](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.51)) by running the following commands: ```console diff --git a/docs/meta/wg_onto/used-ontologies/nfdixcs.md b/docs/meta/wg_onto/used-ontologies/nfdixcs.md index aa5985c..2f0d660 100644 --- a/docs/meta/wg_onto/used-ontologies/nfdixcs.md +++ b/docs/meta/wg_onto/used-ontologies/nfdixcs.md @@ -2,7 +2,8 @@ title: NFDIxCS --- -This consortia has not yet created an ontology list. +A collection of ontologies, controlled vocabularies, and schemas relevant for +the NFDIxCS Consortium. ## Maintainers @@ -11,10 +12,38 @@ This consortia has not yet created an ontology list. Suggest a new addition to this collection [here](https://github.com/biopragmatics/bioregistry/issues/new?template=add-collection-prefix.yml&collection=0000035&title=Add%20prefix%20X%20to%20collection%200000035). +## Ontologies + +The following table comes from Semantic Farm collection +[`0000035`](https://semantic.farm/collection/0000035), which is automatically +synced from the TIB Terminology Service collection +[`nfdixcs`](https://service.tib.eu/terminology/collections/nfdixcs). + +| Prefix | Name | License | +| -------------------------------------------------- | -------------------------------------------------------------- | ---------- | +| [`amv`](https://semantic.farm/amv) | Algorithm Metadata Vocabulary | CC0-1.0 | +| [`BFO`](https://semantic.farm/bfo) | Basic Formal Ontology | CC-BY-4.0 | +| [`CiTO`](https://semantic.farm/cito) | Citation Typing Ontology | CC-BY-4.0 | +| [`cso`](https://semantic.farm/cso) | Computer Science Ontology | | +| [`DataCite`](https://semantic.farm/datacite) | DataCite Ontology | | +| [`dblp.schema`](https://semantic.farm/dblp.schema) | DBLP Schema | | +| [`dcterms`](https://semantic.farm/dcterms) | Dublin Core Metadata Initiative Terms | | +| [`doap`](https://semantic.farm/doap) | Description of a Project | Apache-2.0 | +| [`fabio`](https://semantic.farm/fabio) | FaBiO, the FRBR-aligned Bibliographic Ontology | CC-BY-4.0 | +| [`gufo`](https://semantic.farm/gufo) | Unified Foundational Ontology | CC-BY-4.0 | +| [`hpc`](https://semantic.farm/hpc) | High-Performance Computing Ontology | CC-BY-4.0 | +| [`IAO`](https://semantic.farm/iao) | Information Artifact Ontology | CC-BY-4.0 | +| [`infosecsos`](https://semantic.farm/infosecsos) | InfoSecSoS Ontology | | +| [`iotlite`](https://semantic.farm/iotlite) | IoT lite Ontology | CC-BY-3.0 | +| [`mathmoddb`](https://semantic.farm/mathmoddb) | MathModDB Ontology and Knowledge Graph for Mathematical Models | CC-BY-4.0 | +| [`schema`](https://semantic.farm/schema) | Schema.org | | +| [`seon`](https://semantic.farm/seon) | Software Engineering Ontology Network | | +| [`SWO`](https://semantic.farm/swo) | Software Ontology | CC-BY-4.0 | + ## Colophon -This page was automatically generated on 2026-05-07 using Semantic Farm -([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +This page was automatically generated on 2026-05-08 using Semantic Farm +([v0.13.51](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.51)) by running the following commands: ```console diff --git a/docs/meta/wg_onto/used-ontologies/punch4nfdi.md b/docs/meta/wg_onto/used-ontologies/punch4nfdi.md index b23f336..4168627 100644 --- a/docs/meta/wg_onto/used-ontologies/punch4nfdi.md +++ b/docs/meta/wg_onto/used-ontologies/punch4nfdi.md @@ -13,8 +13,8 @@ Suggest a new addition to this collection ## Colophon -This page was automatically generated on 2026-05-07 using Semantic Farm -([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +This page was automatically generated on 2026-05-08 using Semantic Farm +([v0.13.51](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.51)) by running the following commands: ```console diff --git a/docs/meta/wg_onto/used-ontologies/text-plus.md b/docs/meta/wg_onto/used-ontologies/text-plus.md index 15ba32e..c7724bf 100644 --- a/docs/meta/wg_onto/used-ontologies/text-plus.md +++ b/docs/meta/wg_onto/used-ontologies/text-plus.md @@ -40,8 +40,8 @@ The following table comes from Semantic Farm collection ## Colophon -This page was automatically generated on 2026-05-07 using Semantic Farm -([v0.13.50](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.50)) +This page was automatically generated on 2026-05-08 using Semantic Farm +([v0.13.51](https://github.com/biopragmatics/bioregistry/releases/tag/v0.13.51)) by running the following commands: ```console diff --git a/scripts/update_collections.py b/scripts/update_collections.py index dae9434..987357c 100644 --- a/scripts/update_collections.py +++ b/scripts/update_collections.py @@ -1,7 +1,7 @@ # /// script # requires-python = ">=3.14" # dependencies = [ -# "bioregistry>=0.13.50", +# "bioregistry>=0.13.51", # "click>=8.3.2", # "tabulate>=0.10.0", # ] @@ -28,7 +28,7 @@ VERSION = bioregistry.version.get_version() V_LINK = f"Semantic Farm ([v{VERSION}](https://github.com/biopragmatics/bioregistry/releases/tag/v{VERSION}))" -RENAMES = {"text+": "text-plus", "berd@nfdi": "berd-nfdi", "ndfi4cat": "nfdi4cat"} +RENAMES = {"text+": "text-plus", "berd@nfdi": "berd-nfdi"} COLOPHON = f""" ## Colophon @@ -75,7 +75,7 @@ def main() -> None: The NFDI Section Metadata Working Group on Ontology Harmonization and Mapping has generated an overview of the ontologies, terminologies, controlled vocabularies, and related semantic artifacts used by each consortium. - + We first partnered with members of each consortium to collaboratively construct their respective collections in the [Semantic Farm](https://semantic.farm), a comprehensive registry of ontologies, terminologies, controlled vocabularies, and related semantic