Published November 8, 2022
| Version v3.1.0
Software
Open
Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science
Authors/Creators
- Unni, Deepak R.
- Moxon, Sierra A. T.
- Bada, Michael
- Brush, Matthew
- Bruskiewich, Richard
- Caufield, J. Harry
- Clemons, Paul A.
- Dancik, Vlado
- Dumontier, Michel
- Fecho, Karamarie
- Glusman, Gustavo
- Hadlock, Jennifer J.
- Harris, Nomi L.
- Joshi, Arpita
- Putman, Tim
- Qin, Guangrong
- Ramsey, Stephen A.
- Shefchek, Kent A.
- Solbrig, Harold
- Soman, Karthik
- Thessen, Anne E.
- Haendel, Melissa A.
- Bizon, Chris
- Mungall, Christopher J.
- Acevedo, Liliana
- Ahalt, Stanley C.
- Alden, John
- Alkanaq, Ahmed
- Amin, Nada
- Avila, Ricardo
- Balhoff, Jim
- Baranzini, Sergio E.
- Baumgartner, Andrew
- Baumgartner, William
- Belhu, Basazin
- Brandes, MacKenzie
- Brandon, Namdi
- Burtt, Noel
- Byrd, William
- Callaghan, Jackson
- Cano, Marco Alvarado
- Carrell, Steven
- Celebi, Remzi
- Champion, James
- Chen, Zhehuan
- Chen, Mei‐Jan
- Chung, Lawrence
- Cohen, Kevin
- Conlin, Tom
- Corkill, Dan
- Costanzo, Maria
- Cox, Steven
- Crouse, Andrew
- Crowder, Camerron
- Crumbley, Mary E.
- Dai, Cheng
- Dančík, Vlado
- De Miranda Azevedo, Ricardo
- Deutsch, Eric
- Dougherty, Jennifer
- Duby, Marc P.
- Duvvuri, Venkata
- Edwards, Stephen
- Emonet, Vincent
- Fehrmann, Nathaniel
- Flannick, Jason
- Foksinska, Aleksandra M.
- Gardner, Vicki
- Gatica, Edgar
- Glen, Amy
- Goel, Prateek
- Gormley, Joseph
- Greyber, Alon
- Haaland, Perry
- Hanspers, Kristina
- He, Kaiwen
- He, Kaiwen
- Henrickson, Jeff
- Hinderer, Eugene W.
- Hoatlin, Maureen
- Hoffman, Andrew
- Huang, Sui
- Huang, Conrad
- Hubal, Robert
- Huellas‐Bruskiewicz, Kenneth
- Huls, Forest B.
- Hunter, Lawrence
- Hyde, Greg
- Issabekova, Tursynay
- Jarrell, Matthew
- Jenkins, Lindsay
- Johs, Adam
- Kang, Jimin
- Kanwar, Richa
- Kebede, Yaphet
- Kim, Keum Joo
- Kluge, Alexandria
- Knowles, Michael
- Koesterer, Ryan
- Korn, Daniel
- Koslicki, David
- Krishnamurthy, Ashok
- Kvarfordt, Lindsey
- Lee, Jay
- Leigh, Margaret
- Lin, Jason
- Liu, Zheng
- Liu, Shaopeng
- Ma, Chunyu
- Magis, Andrew
- Mamidi, Tarun
- Mandal, Meisha
- Mantilla, Michelle
- Massung, Jeffrey
- Mauldin, Denise
- McClelland, Jason
- McMurry, Julie
- Mease, Philip
- Mendoza, Luis
- Mersmann, Marian
- Mesbah, Abrar
- Might, Matthew
- Morton, Kenny
- Muller, Sandrine
- Muluka, Arun Teja
- Osborne, John
- Owen, Phil
- Patton, Michael
- Peden, David B.
- Peene, R. Carter
- Persaud, Bria
- Pfaff, Emily
- Pico, Alexander
- Pollard, Elizabeth
- Price, Guthrie
- Raj, Shruti
- Reilly, Jason
- Riutta, Anders
- Roach, Jared
- Roper, Ryan T.
- Rosenblatt, Greg
- Rubin, Irit
- Rucka, Sienna
- Rudavsky‐Brody, Nathaniel
- Sakaguchi, Rayn
- Santos, Eugene
- Schaper, Kevin
- Schmitt, Charles P.
- Schurman, Shepherd
- Scott, Erik
- Seitanakis, Sarah
- Sharma, Priya
- Shmulevich, Ilya
- Shrestha, Manil
- Shrivastava, Shalki
- Sinha, Meghamala
- Smith, Brett
- Southall, Noel
- Southern, Nicholas
- Stillwell, Lisa
- Strasser, Michael " Michi"
- Su, Andrew I.
- Ta, Casey
- Thessen, Anne E.
- Tinglin, Jillian
- Tonstad, Lucas
- Tran‐Nguyen, Thi
- Tropsha, Alexander
- Vaidya, Gaurav
- Veenhuis, Luke
- Viola, Adam
- Grotthuss, Marcin
- Wang, Max
- Wang, Patrick
- Watkins, Paul B.
- Weber, Rosina
- Wei, Qi
- Weng, Chunhua
- Whitlock, Jordan
- Williams, Mark D.
- Williams, Andrew
- Womack, Finn
- Wood, Erica
- Wu, Chunlei
- Xin, Jiwen Kevin
- Xu, Hao
- Xu, Colleen
- Yakaboski, Chase
- Yao, Yao
- Yi, Hong
- Yilmaz, Arif
- Zheng, Marissa
- Zhou, Xinghua
- Zhou, Eric
- Zhu, Qian
- Zisk, Tom
Description
What's Changed
- Some (new?) inverse predicates are missing their is_a property connection to the predicate hierarchy by @RichardBruskiewich in https://github.com/biolink/biolink-model/pull/1095
- Updating biolink-model.yaml to include new classes for epigenomic ent… by @beasleyjonm in https://github.com/biolink/biolink-model/pull/1102
- fixes #1111 - exposure_event is_a: ontology_class by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1113
- fixes #1101, fixes #1100, fixes #1098 add subject of investigation mixin to many different organism level c… by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1115
- Association and Predicates for Gene to Gene Family relationships by @RichardBruskiewich in https://github.com/biolink/biolink-model/pull/945
- Supporting publications fixes #1107 by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1114
- remove obsolete GAMMA predicates by @EvanDietzMorris in https://github.com/biolink/biolink-model/pull/1117
- Move deprecated mappings to examples/biolink3_migration/predicate_mappings.yaml by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1116
- fixes #1088 - make macromolecular complex a class, add mappings by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1125
- fixes #1096 - add Study, Variable, CommonDataElement by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1126
- fixes #1124 adding canonical tags to response predicates, deprecating increase/de… by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1127
- updating orphanet prefix, fixes #1122 by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1128
- fixes #1119 by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1129
- remove mixin tag from regulates, fixes #1094 by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1130
- adding documentation and examples on qualifiers partially fixes #1133 by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1134
- fixing unknown prefix artifact regeneration error by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1135
- update doc gen to not include yamlfile by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1136
- replace spaces with underscores in enumerations by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1137
- add infores catalog as a nodes tsv file by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1139
- fixes #1132 : include mappings and id prefixes for "chemical role" by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1142
- refactor Sequence Variant to make it more clear that CNVs are a sublc… by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1141
- refactor helpdesk template to include contact information, fixes #1138 by @sierra-moxon in https://github.com/biolink/biolink-model/pull/1146
- @beasleyjonm made their first contribution in https://github.com/biolink/biolink-model/pull/1102
- @EvanDietzMorris made their first contribution in https://github.com/biolink/biolink-model/pull/1117
Full Changelog: https://github.com/biolink/biolink-model/compare/v3.0.3...v3.1.0
Notes
Please cite the following works when using this software.
Files
biolink/biolink-model-v3.1.0.zip
Files
(4.7 MB)
| Name | Size | Download all |
|---|---|---|
|
md5:849f3b473482bfafa77e7079f45ff9cd
|
4.7 MB | Preview Download |
Additional details
Related works
- Is supplement to
- https://github.com/biolink/biolink-model/tree/v3.1.0 (URL)