indra_cogex/bdf.yaml at main · haohangyan/indra_cogex · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
version: v0.0.1

tool:
  name: INDRA
  repo_url: https://github.com/gyorilab/indra_cogex
  package_url: https://pypi.org/project/indra
  tool_homepage: https://discovery.indra.bio
  documentation_url: https://indra.readthedocs.io/en/latest/installation.html
  tool_type: Library

llm:
  usesLlm: true
  modelsSupported:
    - openai
  modelsRequired:
    - openai
  bringOwnKey: false

input:
  - name: omics/molecular unstructured 1
    dataCategory: omics-molecular
    dataClass: unstructured-text
    dataType: Publications
    format:
      - txt
    dataStandard:
      - unknown
    proprietary: false
    source:
  - name: omics/molecular structured 1
    dataCategory: omics-molecular
    dataClass: structured
    dataType: Multiple structured databases (not raw data)
    format:
      - various
    dataStandard:
      - BioPAX
      - PSI-ML
      - BEL
      - various non-standard formats
    proprietary: false
    source:
  - name: omics/molecular tabular 1
    dataCategory: omics-molecular
    dataClass: tabular
    dataType: proteomics
    format:
      - csv
    dataStandard:
      - unknown
    proprietary: false
    source:

output:
  - name: Knowledge Graph 1
    dataCategory: knowledge graph
    dataClass: graph-or-network
    dataType: unknown
    format:
      - json
    dataStandard:
      - unknown
    proprietary: false
    source:
  - name: Interpretation results 1
    dataCategory: interpretation results
    dataClass: tabular
    dataType: enrichment, evidence from knowledge graph
    format:
      - csv
    dataStandard:
      - unknown
    proprietary: false
    source:

collaborations: []

domains:
  - omics data interpretation

credit:
  - name: NEU ASKEM Team
    role: Developer
    org: Northeastern University
    url: https://gyorilab.github.io/

maturity:
  beginning_maturity: 1
  current_maturity: 6

license:
  license_type: BSD-2-Clause
  link: https://github.com/gyorilab/indra_cogex/blob/main/LICENSE

target_users:
  primary_user:
    user_type: researcher
    technical_literacy_level:
      - intermediate
    biomedical_literacy_level:
      - intermediate

media: []