biolink-model

Schema and generated objects for biolink data model and upper ontology

https://github.com/biolink/biolink-model

Science Score: 77.0%

This score indicates how likely this project is to be science-related based on various indicators:

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 1 DOI reference(s) in README
✓
Academic publication links
Links to: wiley.com, zenodo.org
✓
Committers with academic emails
5 of 57 committers (8.8%) from academic institutions
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (11.0%) to scientific vocabulary

Keywords

biolink datamodel gene-ontology json-api knowledge-graphs linkml monarchinitiative ncats ncats-translator neo4j obofoundry owl rdf specification standard yaml

Keywords from Contributors

semantic-web json-schema standards linked-data shacl data-modeling shex ontology data-dictionaries json-ld-context

Last synced: 6 months ago · JSON representation ·

Repository

Schema and generated objects for biolink data model and upper ontology

Basic Info

Host: GitHub
Owner: biolink
License: other
Language: Python
Default Branch: master
Homepage: https://biolink.github.io/biolink-model/
Size: 311 MB

Statistics

Stars: 201
Watchers: 24
Forks: 80
Open Issues: 153
Releases: 103

Topics

biolink datamodel gene-ontology json-api knowledge-graphs linkml monarchinitiative ncats ncats-translator neo4j obofoundry owl rdf specification standard yaml

Created about 8 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog License Code of conduct Citation Authors

Biolink Model

Biolink Model: https://w3id.org/biolink/biolink-model.yaml

Quickstart docs:

For a good overview of the biolink-model, watch Chris Mungall's talk at ICBO 2020.

Browse the model: https://biolink.github.io/biolink-model

Refer to the following resources for a quick introduction to the Biolink Model: - Introduction to the Biolink Datamodel - Biolink Model - A community driven data model for life sciences (Biocuration 2020) - Slides: https://bit.ly/biolink-model-workshop-biocuration-2020 - Video: https://www.youtube.com/watch?v=RE1hFm8lvJA

See also the Biolink Model Documentation for help in understanding, curating, and working with the model.

Introduction

The purpose of the Biolink Model is to provide a high-level datamodel of biological entities (genes, diseases, phenotypes, pathways, individuals, substances, etc), their properties, relationships, and enumerate ways in which they can be associated.

The representation is independent of storage technology or metamodel (Solr documents, neo4j/property graphs, RDF/OWL, JSON, CSVs, etc). Different mappings to each of these are provided.

The specification of the Biolink Model is a single YAML file built using linkml. The basic elements of the YAML are:

Class Definitions: definitions of upper level classes representing both 'named thing' and 'association'
Slot Definitions: definitions of slots (aka properties) that can be used to relate members of these classes to other classes or data types. Slots collectively refer to predicates, node properties, and edge properties

The model itself is being used in the following projects: - NCATS Biomedical Data Translator - Monarch Initiative - KG-COVID-19 - KG Microbe - Illuminating the Druggable Genome

Organization

The main source of truth is biolink-model.yaml. This is a YAML file that is intended to be relatively simple to view and edit in its native form.

The yaml definition is currently used to derive:

Citing Biolink Model

Unni DR, Moxon SAT, Bada M, Brush M, Bruskiewich R, Caufield JH, Clemons PA, Dancik V, Dumontier M, Fecho K, Glusman G, Hadlock JJ, Harris NL, Joshi A, Putman T, Qin G, Ramsey SA, Shefchek KA, Solbrig H, Soman K, Thessen AE, Haendel MA, Bizon C, Mungall CJ, The Biomedical Data Translator Consortium (2022). Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science. Clin Transl Sci. Wiley; 2022 Jun 6; https://onlinelibrary.wiley.com/doi/10.1111/cts.13302

Owner

Name: biolink
Login: biolink
Kind: organization

Repositories: 10
Profile: https://github.com/biolink

Citation (CITATION.cff)

cff-version: '1.1.0'
message: 'Please cite the following works when using this software.'
authors:
  - family-names: 'Unni'
    given-names: 'Deepak R.'
  - family-names: 'Moxon'
    given-names: 'Sierra A. T.'
  - family-names: 'Bada'
    given-names: 'Michael'
  - family-names: 'Brush'
    given-names: 'Matthew'
  - family-names: 'Bruskiewich'
    given-names: 'Richard'
  - family-names: 'Caufield'
    given-names: 'J. Harry'
  - family-names: 'Clemons'
    given-names: 'Paul A.'
  - family-names: 'Dancik'
    given-names: 'Vlado'
  - family-names: 'Dumontier'
    given-names: 'Michel'
  - family-names: 'Fecho'
    given-names: 'Karamarie'
  - family-names: 'Glusman'
    given-names: 'Gustavo'
  - family-names: 'Hadlock'
    given-names: 'Jennifer J.'
  - family-names: 'Harris'
    given-names: 'Nomi L.'
  - family-names: 'Joshi'
    given-names: 'Arpita'
  - family-names: 'Putman'
    given-names: 'Tim'
  - family-names: 'Qin'
    given-names: 'Guangrong'
  - family-names: 'Ramsey'
    given-names: 'Stephen A.'
  - family-names: 'Shefchek'
    given-names: 'Kent A.'
  - family-names: 'Solbrig'
    given-names: 'Harold'
  - family-names: 'Soman'
    given-names: 'Karthik'
  - family-names: 'Thessen'
    given-names: 'Anne E.'
  - family-names: 'Haendel'
    given-names: 'Melissa A.'
  - family-names: 'Bizon'
    given-names: 'Chris'
  - family-names: 'Mungall'
    given-names: 'Christopher J.'
  - family-names: 'Acevedo'
    given-names: 'Liliana'
  - family-names: 'Ahalt'
    given-names: 'Stanley C.'
  - family-names: 'Alden'
    given-names: 'John'
  - family-names: 'Alkanaq'
    given-names: 'Ahmed'
  - family-names: 'Amin'
    given-names: 'Nada'
  - family-names: 'Avila'
    given-names: 'Ricardo'
  - family-names: 'Balhoff'
    given-names: 'Jim'
  - family-names: 'Baranzini'
    given-names: 'Sergio E.'
  - family-names: 'Baumgartner'
    given-names: 'Andrew'
  - family-names: 'Baumgartner'
    given-names: 'William'
  - family-names: 'Belhu'
    given-names: 'Basazin'
  - family-names: 'Brandes'
    given-names: 'MacKenzie'
  - family-names: 'Brandon'
    given-names: 'Namdi'
  - family-names: 'Burtt'
    given-names: 'Noel'
  - family-names: 'Byrd'
    given-names: 'William'
  - family-names: 'Callaghan'
    given-names: 'Jackson'
  - family-names: 'Cano'
    given-names: 'Marco Alvarado'
  - family-names: 'Carrell'
    given-names: 'Steven'
  - family-names: 'Celebi'
    given-names: 'Remzi'
  - family-names: 'Champion'
    given-names: 'James'
  - family-names: 'Chen'
    given-names: 'Zhehuan'
  - family-names: 'Chen'
    given-names: 'Mei‐Jan'
  - family-names: 'Chung'
    given-names: 'Lawrence'
  - family-names: 'Cohen'
    given-names: 'Kevin'
  - family-names: 'Conlin'
    given-names: 'Tom'
  - family-names: 'Corkill'
    given-names: 'Dan'
  - family-names: 'Costanzo'
    given-names: 'Maria'
  - family-names: 'Cox'
    given-names: 'Steven'
  - family-names: 'Crouse'
    given-names: 'Andrew'
  - family-names: 'Crowder'
    given-names: 'Camerron'
  - family-names: 'Crumbley'
    given-names: 'Mary E.'
  - family-names: 'Dai'
    given-names: 'Cheng'
  - family-names: 'Dančík'
    given-names: 'Vlado'
  - family-names: 'De Miranda Azevedo'
    given-names: 'Ricardo'
  - family-names: 'Deutsch'
    given-names: 'Eric'
  - family-names: 'Dougherty'
    given-names: 'Jennifer'
  - family-names: 'Duby'
    given-names: 'Marc P.'
  - family-names: 'Duvvuri'
    given-names: 'Venkata'
  - family-names: 'Edwards'
    given-names: 'Stephen'
  - family-names: 'Emonet'
    given-names: 'Vincent'
  - family-names: 'Fehrmann'
    given-names: 'Nathaniel'
  - family-names: 'Flannick'
    given-names: 'Jason'
  - family-names: 'Foksinska'
    given-names: 'Aleksandra M.'
  - family-names: 'Gardner'
    given-names: 'Vicki'
  - family-names: 'Gatica'
    given-names: 'Edgar'
  - family-names: 'Glen'
    given-names: 'Amy'
  - family-names: 'Goel'
    given-names: 'Prateek'
  - family-names: 'Gormley'
    given-names: 'Joseph'
  - family-names: 'Greyber'
    given-names: 'Alon'
  - family-names: 'Haaland'
    given-names: 'Perry'
  - family-names: 'Hanspers'
    given-names: 'Kristina'
  - family-names: 'He'
    given-names: 'Kaiwen'
  - family-names: 'He'
    given-names: 'Kaiwen'
  - family-names: 'Henrickson'
    given-names: 'Jeff'
  - family-names: 'Hinderer'
    given-names: 'Eugene W.'
  - family-names: 'Hoatlin'
    given-names: 'Maureen'
  - family-names: 'Hoffman'
    given-names: 'Andrew'
  - family-names: 'Huang'
    given-names: 'Sui'
  - family-names: 'Huang'
    given-names: 'Conrad'
  - family-names: 'Hubal'
    given-names: 'Robert'
  - family-names: 'Huellas‐Bruskiewicz'
    given-names: 'Kenneth'
  - family-names: 'Huls'
    given-names: 'Forest B.'
  - family-names: 'Hunter'
    given-names: 'Lawrence'
  - family-names: 'Hyde'
    given-names: 'Greg'
  - family-names: 'Issabekova'
    given-names: 'Tursynay'
  - family-names: 'Jarrell'
    given-names: 'Matthew'
  - family-names: 'Jenkins'
    given-names: 'Lindsay'
  - family-names: 'Johs'
    given-names: 'Adam'
  - family-names: 'Kang'
    given-names: 'Jimin'
  - family-names: 'Kanwar'
    given-names: 'Richa'
  - family-names: 'Kebede'
    given-names: 'Yaphet'
  - family-names: 'Kim'
    given-names: 'Keum Joo'
  - family-names: 'Kluge'
    given-names: 'Alexandria'
  - family-names: 'Knowles'
    given-names: 'Michael'
  - family-names: 'Koesterer'
    given-names: 'Ryan'
  - family-names: 'Korn'
    given-names: 'Daniel'
  - family-names: 'Koslicki'
    given-names: 'David'
  - family-names: 'Krishnamurthy'
    given-names: 'Ashok'
  - family-names: 'Kvarfordt'
    given-names: 'Lindsey'
  - family-names: 'Lee'
    given-names: 'Jay'
  - family-names: 'Leigh'
    given-names: 'Margaret'
  - family-names: 'Lin'
    given-names: 'Jason'
  - family-names: 'Liu'
    given-names: 'Zheng'
  - family-names: 'Liu'
    given-names: 'Shaopeng'
  - family-names: 'Ma'
    given-names: 'Chunyu'
  - family-names: 'Magis'
    given-names: 'Andrew'
  - family-names: 'Mamidi'
    given-names: 'Tarun'
  - family-names: 'Mandal'
    given-names: 'Meisha'
  - family-names: 'Mantilla'
    given-names: 'Michelle'
  - family-names: 'Massung'
    given-names: 'Jeffrey'
  - family-names: 'Mauldin'
    given-names: 'Denise'
  - family-names: 'McClelland'
    given-names: 'Jason'
  - family-names: 'McMurry'
    given-names: 'Julie'
  - family-names: 'Mease'
    given-names: 'Philip'
  - family-names: 'Mendoza'
    given-names: 'Luis'
  - family-names: 'Mersmann'
    given-names: 'Marian'
  - family-names: 'Mesbah'
    given-names: 'Abrar'
  - family-names: 'Might'
    given-names: 'Matthew'
  - family-names: 'Morton'
    given-names: 'Kenny'
  - family-names: 'Muller'
    given-names: 'Sandrine'
  - family-names: 'Muluka'
    given-names: 'Arun Teja'
  - family-names: 'Osborne'
    given-names: 'John'
  - family-names: 'Owen'
    given-names: 'Phil'
  - family-names: 'Patton'
    given-names: 'Michael'
  - family-names: 'Peden'
    given-names: 'David B.'
  - family-names: 'Peene'
    given-names: 'R. Carter'
  - family-names: 'Persaud'
    given-names: 'Bria'
  - family-names: 'Pfaff'
    given-names: 'Emily'
  - family-names: 'Pico'
    given-names: 'Alexander'
  - family-names: 'Pollard'
    given-names: 'Elizabeth'
  - family-names: 'Price'
    given-names: 'Guthrie'
  - family-names: 'Raj'
    given-names: 'Shruti'
  - family-names: 'Reilly'
    given-names: 'Jason'
  - family-names: 'Riutta'
    given-names: 'Anders'
  - family-names: 'Roach'
    given-names: 'Jared'
  - family-names: 'Roper'
    given-names: 'Ryan T.'
  - family-names: 'Rosenblatt'
    given-names: 'Greg'
  - family-names: 'Rubin'
    given-names: 'Irit'
  - family-names: 'Rucka'
    given-names: 'Sienna'
  - family-names: 'Rudavsky‐Brody'
    given-names: 'Nathaniel'
  - family-names: 'Sakaguchi'
    given-names: 'Rayn'
  - family-names: 'Santos'
    given-names: 'Eugene'
  - family-names: 'Schaper'
    given-names: 'Kevin'
  - family-names: 'Schmitt'
    given-names: 'Charles P.'
  - family-names: 'Schurman'
    given-names: 'Shepherd'
  - family-names: 'Scott'
    given-names: 'Erik'
  - family-names: 'Seitanakis'
    given-names: 'Sarah'
  - family-names: 'Sharma'
    given-names: 'Priya'
  - family-names: 'Shmulevich'
    given-names: 'Ilya'
  - family-names: 'Shrestha'
    given-names: 'Manil'
  - family-names: 'Shrivastava'
    given-names: 'Shalki'
  - family-names: 'Sinha'
    given-names: 'Meghamala'
  - family-names: 'Smith'
    given-names: 'Brett'
  - family-names: 'Southall'
    given-names: 'Noel'
  - family-names: 'Southern'
    given-names: 'Nicholas'
  - family-names: 'Stillwell'
    given-names: 'Lisa'
  - family-names: 'Strasser'
    given-names: 'Michael " Michi"'
  - family-names: 'Su'
    given-names: 'Andrew I.'
  - family-names: 'Ta'
    given-names: 'Casey'
  - family-names: 'Thessen'
    given-names: 'Anne E.'
  - family-names: 'Tinglin'
    given-names: 'Jillian'
  - family-names: 'Tonstad'
    given-names: 'Lucas'
  - family-names: 'Tran‐Nguyen'
    given-names: 'Thi'
  - family-names: 'Tropsha'
    given-names: 'Alexander'
  - family-names: 'Vaidya'
    given-names: 'Gaurav'
  - family-names: 'Veenhuis'
    given-names: 'Luke'
  - family-names: 'Viola'
    given-names: 'Adam'
  - family-names: 'Grotthuss'
    given-names: 'Marcin'
  - family-names: 'Wang'
    given-names: 'Max'
  - family-names: 'Wang'
    given-names: 'Patrick'
  - family-names: 'Watkins'
    given-names: 'Paul B.'
  - family-names: 'Weber'
    given-names: 'Rosina'
  - family-names: 'Wei'
    given-names: 'Qi'
  - family-names: 'Weng'
    given-names: 'Chunhua'
  - family-names: 'Whitlock'
    given-names: 'Jordan'
  - family-names: 'Williams'
    given-names: 'Mark D.'
  - family-names: 'Williams'
    given-names: 'Andrew'
  - family-names: 'Womack'
    given-names: 'Finn'
  - family-names: 'Wood'
    given-names: 'Erica'
  - family-names: 'Wu'
    given-names: 'Chunlei'
  - family-names: 'Xin'
    given-names: 'Jiwen Kevin'
  - family-names: 'Xu'
    given-names: 'Hao'
  - family-names: 'Xu'
    given-names: 'Colleen'
  - family-names: 'Yakaboski'
    given-names: 'Chase'
  - family-names: 'Yao'
    given-names: 'Yao'
  - family-names: 'Yi'
    given-names: 'Hong'
  - family-names: 'Yilmaz'
    given-names: 'Arif'
  - family-names: 'Zheng'
    given-names: 'Marissa'
  - family-names: 'Zhou'
    given-names: 'Xinghua'
  - family-names: 'Zhou'
    given-names: 'Eric'
  - family-names: 'Zhu'
    given-names: 'Qian'
  - family-names: 'Zisk'
    given-names: 'Tom'
doi: '10.1111/cts.13302'
identifiers:
  - type: 'doi'
    value: '10.1111/cts.13302'
  - type: 'url'
    value: 'http://dx.doi.org/10.1111/cts.13302'
  - type: 'other'
    value: 'urn:issn:1752-8054'
title: 'Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science'
url: 'http://dx.doi.org/10.1111/cts.13302'

GitHub Events

Total

Create event: 30
Release event: 6
Issues event: 20
Watch event: 26
Delete event: 8
Issue comment event: 80
Member event: 2
Push event: 105
Pull request review comment event: 19
Pull request review event: 33
Pull request event: 68
Fork event: 6

Last Year

Create event: 30
Release event: 6
Issues event: 20
Watch event: 26
Delete event: 8
Issue comment event: 80
Member event: 2
Push event: 105
Pull request review comment event: 19
Pull request review event: 33
Pull request event: 68
Fork event: 6

Committers

Last synced: 9 months ago

All Time

Total Commits: 2,726
Total Committers: 57
Avg Commits per committer: 47.825
Development Distribution Score (DDS): 0.558

Past Year

Commits: 113
Committers: 11
Avg Commits per committer: 10.273
Development Distribution Score (DDS): 0.637

Top Committers

Name	Email	Commits
Sierra Taylor Moxon	s**r@g**m	1,205
GitHub Action	a**n@g**m	277
Deepak Unni	d**3@g**m	271
Richard Bruskiewich	r**d@s**m	196
cmungall	c**m@b**g	159
Richard Bruskiewich	r**h@d**m	121
hsolbrig	s**g@j**u	121
Kevin Schaper	k**r@g**m	51
cbizon	b**n@r**g	43
Matthew Brush	m**0@g**m	37
Colleen Xu	c**u@g**m	30
dependabot[bot]	4****]	21
obophenotype	o**d@e**g	16
Nomi Harris	n****s	15
YaphetKG	k**y@r**g	11
Lance Hannestad	l****t	11
Vincent Vialard	v**d@d**e	10
Jim Balhoff	b**f@g**m	10
Evan Morris	e**s@g**m	9
kshefchek	k**k@g**m	9
cmungall	c**l@g**m	8
Anne Thessen	a**n@g**m	7
Gaurav Vaidya	g**v@r**g	7
Vincent Emonet	v**t@g**m	6
Yaroslav Halchenko	d**n@o**m	6
beasleyjonm	8****m	6
karafecho	k**o@c**m	6
Andrew Su	a**u@g**m	5
Guangrong Qin	g**6@g**m	5
iQuxLE	c**5@g**m	4
and 27 more...

Committer Domains (Top 20 + Academic)

renci.org: 3 scripps.edu: 2 covar.com: 2 github.com: 1 starinformatics.com: 1 berkeleybop.org: 1 delphinai.com: 1 jhu.edu: 1 example.org: 1 derivo.de: 1 onerussian.com: 1 copperlineprofessionalsolutions.com: 1 altoslabs.com: 1 sib.swiss: 1 lirmm.fr: 1 bmahq.com: 1 email.unc.edu: 1 gitter.im: 1 oregonstate.edu: 1 isbscience.org: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 150
Total pull requests: 325
Average time to close issues: 7 months
Average time to close pull requests: 13 days
Total issue authors: 43
Total pull request authors: 35
Average comments per issue: 1.97
Average comments per pull request: 0.39
Merged pull requests: 283
Bot issues: 0
Bot pull requests: 34

Past Year

Issues: 19
Pull requests: 82
Average time to close issues: 6 days
Average time to close pull requests: 12 days
Issue authors: 14
Pull request authors: 11
Average comments per issue: 0.37
Average comments per pull request: 0.54
Merged pull requests: 58
Bot issues: 0
Bot pull requests: 11

View more stats

Top Authors

Issue Authors

sierra-moxon (26)
vincentvialard (12)
cbizon (8)
gaurav (8)
vdancik (7)
RichardBruskiewich (7)
kevinschaper (6)
mbrush (6)
cmungall (6)
balhoff (5)
colleenXu (5)
codewarrior2000 (4)
riyavsinha (4)
karafecho (4)
matentzn (3)

Pull Request Authors

sierra-moxon (147)
kevinschaper (40)
dependabot[bot] (33)
colleenXu (17)
cbizon (12)
mbrush (10)
RichardBruskiewich (6)
karafecho (5)
beasleyjonm (5)
iQuxLE (4)
nicholsn (4)
gaurav (3)
balhoff (3)
EvanDietzMorris (3)
andrewsu (2)

Top Labels

Issue Labels

documentation (33) question (25) enhancement (19) bug (16) identifiers (15) help-desk (11) working-group/predicates (10) working-group/MolePro (9) working-group/chemical (7) next release candidate (6) LinkML (5) mapping (5) working-group/clinical (4) community-generated (4) devops (3) working-group/EPC (2) ARA/exploring-agent (2) working-group/NodeNormalizer (2) translator-monarch-discussion (2) working-group/ROBOKOP (1) exposure (1) kg-hub (1) needs-review (1) QC (1) ARA/expander-agent (1) release-3.6.0 (1) kp/multiomics-provider (1) policy (1) kp/geneticsprovider (1) working-group/KGE (1)

Pull Request Labels

dependencies (33) python (8) help-desk (1) github_actions (1)

Packages

Total packages: 3
Total downloads:
- pypi 2,766 last-month

Total dependent packages: 1
(may contain duplicates)
Total dependent repositories: 5
(may contain duplicates)
Total versions: 155
Total maintainers: 4

pypi.org: biolink-model

The Biolink Model is a high-level data model designed to standardize types and relationships in biological knowledgebases.

Documentation: https://biolink-model.readthedocs.io/
License: MIT
Latest release: 4.2.5
published over 1 year ago

Versions: 75
Dependent Packages: 0
Dependent Repositories: 4
Downloads: 2,725 Last month

Rankings

Forks count: 5.3%

Stargazers count: 5.9%

Average: 7.2%

Dependent packages count: 7.3%

Dependent repos count: 7.6%

Downloads: 9.9%

Maintainers (4)

cmungall hsolbrig smoxon deepakunni3

Last synced: 6 months ago

proxy.golang.org: github.com/biolink/biolink-model

Documentation: https://pkg.go.dev/github.com/biolink/biolink-model#section-documentation
License: other
Latest release: v4.2.5+incompatible
published over 1 year ago

Versions: 74
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 7.0%

Average: 8.2%

Dependent repos count: 9.3%

Last synced: 6 months ago

pypi.org: biolinkmg

Schema and generated objects for biolink data model and upper ontology

Homepage: https://github.com/biolink/biolink-model
Documentation: https://biolinkmg.readthedocs.io/
License: CC0 1.0 Universal
Latest release: 0.3.0
published about 7 years ago

Versions: 6
Dependent Packages: 1
Dependent Repositories: 1
Downloads: 41 Last month

Rankings

Dependent packages count: 3.2%

Forks count: 5.3%

Stargazers count: 5.9%

Average: 15.1%

Dependent repos count: 22.1%

Downloads: 39.2%

Maintainers (1)

hsolbrig

Last synced: 6 months ago

Dependencies

Pipfile pypi

linkml *

Pipfile.lock pypi

alabaster ==0.7.12
antlr4-python3-runtime ==4.9.3
argparse ==1.4.0
attrs ==21.4.0
babel ==2.10.3
certifi ==2022.6.15
cfgraph ==0.2.1
chardet ==5.0.0
charset-normalizer ==2.1.0
click ==8.1.3
decorator ==5.1.1
deprecated ==1.2.13
docutils ==0.18.1
et-xmlfile ==1.1.0
graphviz ==0.20
greenlet ==1.1.2
hbreader ==0.9.1
idna ==3.3
imagesize ==1.4.1
importlib-metadata ==4.12.0
isodate ==0.6.1
jinja2 ==3.1.2
json-flattener ==0.1.9
jsonasobj ==1.3.1
jsonasobj2 ==1.0.4
jsonpatch ==1.32
jsonpath-ng ==1.5.3
jsonpointer ==2.3
jsonschema ==4.7.2
linkml ==1.3.1
linkml-dataops ==0.1.0
linkml-runtime ==1.3.1
markdown-it-py ==2.1.0
markupsafe ==2.1.1
mdit-py-plugins ==0.3.0
mdurl ==0.1.1
myst-parser ==0.18.0
openpyxl ==3.0.10
packaging ==21.3
parse ==1.19.0
ply ==3.11
prefixcommons ==0.1.11
pydantic ==1.9.1
pygments ==2.12.0
pyjsg ==0.11.10
pyparsing ==3.0.9
pyrsistent ==0.18.1
pyshex ==0.8.1
pyshexc ==0.9.1
python-dateutil ==2.8.2
pytz ==2022.1
pyyaml ==6.0
rdflib ==6.1.1
rdflib-jsonld ==0.6.1
rdflib-shim ==1.0.3
requests ==2.28.1
ruamel.yaml ==0.17.21
ruamel.yaml.clib ==0.2.6
setuptools ==63.2.0
shexjsg ==0.8.2
six ==1.16.0
snowballstemmer ==2.2.0
sparqlslurper ==0.5.1
sparqlwrapper ==2.0.0
sphinx ==5.0.2
sphinx-click ==4.3.0
sphinxcontrib-applehelp ==1.0.2
sphinxcontrib-devhelp ==1.0.2
sphinxcontrib-htmlhelp ==2.0.0
sphinxcontrib-jsmath ==1.0.1
sphinxcontrib-qthelp ==1.0.3
sphinxcontrib-serializinghtml ==1.1.5
sqlalchemy ==1.4.39
typing-extensions ==4.3.0
urllib3 ==1.26.10
watchdog ==2.1.9
wrapt ==1.14.1
zipp ==3.8.1

requirements.txt pypi

linkml *

setup.py pypi

for *

biolink-model

Science Score: 77.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

Biolink Model

Introduction

Organization

Citing Biolink Model

Owner

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: biolink-model

Rankings

Maintainers (4)

proxy.golang.org: github.com/biolink/biolink-model

Rankings

pypi.org: biolinkmg

Rankings

Maintainers (1)

Dependencies