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Recent Releases of https://github.com/biopragmatics/pyobo

https://github.com/biopragmatics/pyobo - v0.12.7

What's Changed

  • Update IANA media types by @cthoyt in https://github.com/biopragmatics/pyobo/pull/428
  • Handle ontology IRI and ontology version IRI by @cthoyt in https://github.com/biopragmatics/pyobo/pull/431

Full Changelog: https://github.com/biopragmatics/pyobo/compare/v0.12.6...v0.12.7

- Python
Published by cthoyt 9 months ago

https://github.com/biopragmatics/pyobo - v0.12.5

What's Changed

  • Add SPDX getter by @cthoyt in https://github.com/biopragmatics/pyobo/pull/406
  • Fix root terms for MeSH source by @cthoyt in https://github.com/biopragmatics/pyobo/pull/410
  • Add IANA media types by @cthoyt in https://github.com/biopragmatics/pyobo/pull/407
  • Update clinical trial terms by @cthoyt in https://github.com/biopragmatics/pyobo/pull/409
  • Add new ChEMBL sources by @cthoyt in https://github.com/biopragmatics/pyobo/pull/336
  • Add function to get text embedding and similarity by @cthoyt in https://github.com/biopragmatics/pyobo/pull/412
  • Remove safe get version by @cthoyt in https://github.com/biopragmatics/pyobo/pull/414
  • Improve WikiPathways ingestion by @cthoyt in https://github.com/biopragmatics/pyobo/pull/416
  • Add additional shortcuts for ontology construction by @cthoyt in https://github.com/biopragmatics/pyobo/pull/415
  • Add tests for exporting valid OWL by @cthoyt in https://github.com/biopragmatics/pyobo/pull/417
  • Improve version handling by @cthoyt in https://github.com/biopragmatics/pyobo/pull/317
  • Cleanup I/O utils by @cthoyt in https://github.com/biopragmatics/pyobo/pull/418
  • Improve version getter functions by @cthoyt in https://github.com/biopragmatics/pyobo/pull/422
  • Fix maintainer lookup by @cthoyt in https://github.com/biopragmatics/pyobo/pull/421
  • Add extra cases to boolean parser by @cthoyt in https://github.com/biopragmatics/pyobo/pull/420
  • Add license URI processing test by @cthoyt in https://github.com/biopragmatics/pyobo/pull/423
  • Continue investigating metadata escaping by @cthoyt in https://github.com/biopragmatics/pyobo/pull/419

Full Changelog: https://github.com/biopragmatics/pyobo/compare/v0.12.4...v0.12.5

- Python
Published by cthoyt 9 months ago

https://github.com/biopragmatics/pyobo - v0.12.4

Full Changelog: https://github.com/biopragmatics/pyobo/compare/v0.12.3...v0.12.4

- Python
Published by cthoyt 9 months ago

https://github.com/biopragmatics/pyobo - v0.12.3

What's Changed

  • Rewrite OBO Graph JSON exporter and implement draft importer by @cthoyt in https://github.com/biopragmatics/pyobo/pull/375
  • Reorganize OBO reader by @cthoyt in https://github.com/biopragmatics/pyobo/pull/403
  • Address QA tests on broken resources by @cthoyt in https://github.com/biopragmatics/pyobo/pull/404
  • Add IntAct source (just with xrefs for now)

Full Changelog: https://github.com/biopragmatics/pyobo/compare/v0.12.2...v0.12.3

- Python
Published by cthoyt about 1 year ago

https://github.com/biopragmatics/pyobo - v0.12.2

What's Changed

  • Externalize processing rules by @cthoyt in https://github.com/biopragmatics/pyobo/pull/400
  • Update contributor role taxonomy source by @cthoyt in https://github.com/biopragmatics/pyobo/pull/401
  • Hide bioontologies imports by @cthoyt in https://github.com/biopragmatics/pyobo/pull/402

Full Changelog: https://github.com/biopragmatics/pyobo/compare/v0.12.1...v0.12.2

- Python
Published by cthoyt about 1 year ago

https://github.com/biopragmatics/pyobo - v0.12.1

What's Changed

  • Reuse upstream preprocessor code by @cthoyt in https://github.com/biopragmatics/pyobo/pull/395
  • Resource updates by @cthoyt in https://github.com/biopragmatics/pyobo/pull/396
  • Add additional preprocessing curations by @cthoyt in https://github.com/biopragmatics/pyobo/pull/398
  • Grouped minor improvements by @cthoyt in https://github.com/biopragmatics/pyobo/pull/397
  • Update cruft by @cthoyt in https://github.com/biopragmatics/pyobo/pull/399

Full Changelog: https://github.com/biopragmatics/pyobo/compare/v0.12.0...v0.12.1

- Python
Published by cthoyt about 1 year ago

https://github.com/biopragmatics/pyobo - v0.12.0

The PyOBO v0.12 release makes a lot of big changes, both to the public and private API, to the way caching is done, and to the way references are validated against the Bioregistry. It removes several unmaintained submodules (e.g., NER tool is fully replaced by gilda, AWS caching is removed), updates some defaults (e.g., close synonym is now default to match OWLAPI).

It also makes many updates to sources and adds new ones.

What's Changed

  • Update to Python 3.10 by @cthoyt in https://github.com/biopragmatics/pyobo/pull/203
  • Enable outputting slim OBO by @cthoyt in https://github.com/biopragmatics/pyobo/pull/202
  • Reuse external robot wrapper by @cthoyt in https://github.com/biopragmatics/pyobo/pull/205
  • Update UMLS synonym type definition loading by @cthoyt in https://github.com/biopragmatics/pyobo/pull/206
  • Update path utilities by @cthoyt in https://github.com/biopragmatics/pyobo/pull/204
  • Add resource-specific remappings by @cthoyt in https://github.com/biopragmatics/pyobo/pull/208
  • Implement GOC standardization by @cthoyt in https://github.com/biopragmatics/pyobo/pull/207
  • Add UniMod custom processor by @cthoyt in https://github.com/biopragmatics/pyobo/pull/209
  • Improve annotation and object property adders by @cthoyt in https://github.com/biopragmatics/pyobo/pull/210
  • Improve synonym type definition inferface by @cthoyt in https://github.com/biopragmatics/pyobo/pull/212
  • Update civic.gene and hgnc sources by @cthoyt in https://github.com/biopragmatics/pyobo/pull/213
  • Enable passing a flag for reprocessing by @cthoyt in https://github.com/biopragmatics/pyobo/pull/214
  • Add explicit exports and sort with ruff --preview by @cthoyt in https://github.com/biopragmatics/pyobo/pull/215
  • Add additional typing requirements by @cthoyt in https://github.com/biopragmatics/pyobo/pull/216
  • Fix serialization of synonym typedef with no name by @cthoyt in https://github.com/biopragmatics/pyobo/pull/217
  • Improve alternative identifier lookup functions by @cthoyt in https://github.com/biopragmatics/pyobo/pull/218
  • Simplify getnameby_curie by @cthoyt in https://github.com/biopragmatics/pyobo/pull/219
  • Update skip list, curated rules, and version processing rules by @cthoyt in https://github.com/biopragmatics/pyobo/pull/220
  • Clean up usage of reference tuples by @cthoyt in https://github.com/biopragmatics/pyobo/pull/221
  • Reuse Reference.from_curie for parsing in typedefs module by @cthoyt in https://github.com/biopragmatics/pyobo/pull/223
  • Improve ontology loading utilities by @cthoyt in https://github.com/biopragmatics/pyobo/pull/222
  • Streamline relation string handling by @cthoyt in https://github.com/biopragmatics/pyobo/pull/224
  • Standardize implementation of Term.from_curie by @cthoyt in https://github.com/biopragmatics/pyobo/pull/225
  • Update database and lookup CLI to use uniform arguments by @cthoyt in https://github.com/biopragmatics/pyobo/pull/226
  • Refactor API interface by @cthoyt in https://github.com/biopragmatics/pyobo/pull/227
  • Update term interface by @cthoyt in https://github.com/biopragmatics/pyobo/pull/228
  • Better sorting and hashing of ontology components by @cthoyt in https://github.com/biopragmatics/pyobo/pull/229
  • Update typedef handling by @cthoyt in https://github.com/biopragmatics/pyobo/pull/230
  • Update CURIE parsing utilities by @cthoyt in https://github.com/biopragmatics/pyobo/pull/231
  • Rename variables by @cthoyt in https://github.com/biopragmatics/pyobo/pull/232
  • Update setting species by @cthoyt in https://github.com/biopragmatics/pyobo/pull/233
  • Add tests for terms and ontology reading by @cthoyt in https://github.com/biopragmatics/pyobo/pull/235
  • Breaking: update handling of properties by @cthoyt in https://github.com/biopragmatics/pyobo/pull/236
  • Add module for GTDB by @jplfaria in https://github.com/biopragmatics/pyobo/pull/234
  • Make data model more explicit by @cthoyt in https://github.com/biopragmatics/pyobo/pull/237
  • Update definition handling by @cthoyt in https://github.com/biopragmatics/pyobo/pull/239
  • Add explicit typedefs for GeoNames and ICD10 by @cthoyt in https://github.com/biopragmatics/pyobo/pull/240
  • Streamline property parsing by @cthoyt in https://github.com/biopragmatics/pyobo/pull/244
  • Add better reference hints when working with properties by @cthoyt in https://github.com/biopragmatics/pyobo/pull/241
  • Improve URI parsing by @cthoyt in https://github.com/biopragmatics/pyobo/pull/242
  • Update MSigDB by @cthoyt in https://github.com/biopragmatics/pyobo/pull/243
  • Reader bug fixes - parent parsing and empty quotes by @cthoyt in https://github.com/biopragmatics/pyobo/pull/245
  • Update SSSOM exporter by @cthoyt in https://github.com/biopragmatics/pyobo/pull/238
  • Streamline URI and CURIE parsing in the reader by @cthoyt in https://github.com/biopragmatics/pyobo/pull/246
  • Simplify construction of synonyms in PyOBO sources by @cthoyt in https://github.com/biopragmatics/pyobo/pull/247
  • Improve synonym and synonym typedef handling by @cthoyt in https://github.com/biopragmatics/pyobo/pull/248
  • Remove global import of requests-ftp by @cthoyt in https://github.com/biopragmatics/pyobo/pull/253
  • Remove canonicalizer by @cthoyt in https://github.com/biopragmatics/pyobo/pull/252
  • Remove usage of deprecated code by @cthoyt in https://github.com/biopragmatics/pyobo/pull/255
  • Improve version handling code in OBO reader by @cthoyt in https://github.com/biopragmatics/pyobo/pull/251
  • Fix reading from compressed OBOs by @cthoyt in https://github.com/biopragmatics/pyobo/pull/256
  • Further consolidate CURIE/URI parsing by @cthoyt in https://github.com/biopragmatics/pyobo/pull/257
  • Reuse Bioregistry's identifier standardization code by @cthoyt in https://github.com/biopragmatics/pyobo/pull/258
  • Improve synonym parser by @cthoyt in https://github.com/biopragmatics/pyobo/pull/249
  • Improve typedef parsing by @cthoyt in https://github.com/biopragmatics/pyobo/pull/259
  • Fix default reference output in OBO flat file format by @cthoyt in https://github.com/biopragmatics/pyobo/pull/261
  • Add GARD as a source by @cthoyt in https://github.com/biopragmatics/pyobo/pull/262
  • Add NLM Catalog and fix default prefix on object properties and annotation properties by @cthoyt in https://github.com/biopragmatics/pyobo/pull/263
  • Add BiGG Metabolite by @samuelbunga in https://github.com/biopragmatics/pyobo/pull/124
  • Implement axioms on relations, object properties, and xrefs by @cthoyt in https://github.com/biopragmatics/pyobo/pull/264
  • Improve root term handling by @cthoyt in https://github.com/biopragmatics/pyobo/pull/266
  • Add helper function for annotating year and update NLM catalog source by @cthoyt in https://github.com/biopragmatics/pyobo/pull/268
  • Update MSigDB, CCLE, BiGG, NLM, and ROR by @cthoyt in https://github.com/biopragmatics/pyobo/pull/269
  • Update cruft by @cthoyt in https://github.com/biopragmatics/pyobo/pull/272
  • Refactor term and typedef models by @cthoyt in https://github.com/biopragmatics/pyobo/pull/273
  • Use None for default specificity by @cthoyt in https://github.com/biopragmatics/pyobo/pull/275
  • Improve type annotations for synonym specificity by @cthoyt in https://github.com/biopragmatics/pyobo/pull/276
  • Use None for default synonym type by @cthoyt in https://github.com/biopragmatics/pyobo/pull/274
  • Improve OBO header handling by @cthoyt in https://github.com/biopragmatics/pyobo/pull/277
  • Implement intersection_of by @cthoyt in https://github.com/biopragmatics/pyobo/pull/278
  • Clean up axiom data structure by @cthoyt in https://github.com/biopragmatics/pyobo/pull/279
  • Add additional features to parser by @cthoyt in https://github.com/biopragmatics/pyobo/pull/280
  • Remove xref-types by @cthoyt in https://github.com/biopragmatics/pyobo/pull/281
  • Delete MANIFEST.in by @cthoyt in https://github.com/biopragmatics/pyobo/pull/283
  • Update mapping output by @cthoyt in https://github.com/biopragmatics/pyobo/pull/282
  • Make use of preferred CURIEs more consistent by @cthoyt in https://github.com/biopragmatics/pyobo/pull/284
  • Import ICD11 MMS codes by @cthoyt in https://github.com/biopragmatics/pyobo/pull/285
  • Generate SSSOM for ICD11 to ICD11 codes by @cthoyt in https://github.com/biopragmatics/pyobo/pull/286
  • Refactor of data and folder structure by @cthoyt in https://github.com/biopragmatics/pyobo/pull/287
  • Initial implement of functional OWL by @cthoyt in https://github.com/biopragmatics/pyobo/pull/271
  • Add doctests to CI by @cthoyt in https://github.com/biopragmatics/pyobo/pull/288
  • Minor updates to sources by @cthoyt in https://github.com/biopragmatics/pyobo/pull/290
  • Update auto-generated ontology CLI by @cthoyt in https://github.com/biopragmatics/pyobo/pull/292
  • Generate IRI and versioned IRI for functional OWL by @cthoyt in https://github.com/biopragmatics/pyobo/pull/289
  • Add prefix consistency check by @cthoyt in https://github.com/biopragmatics/pyobo/pull/293
  • Get all prefixes used in an ontology by @cthoyt in https://github.com/biopragmatics/pyobo/pull/291
  • Update cruft by @cthoyt in https://github.com/biopragmatics/pyobo/pull/295
  • Add source for NCBI Genetic Codes by @cthoyt in https://github.com/biopragmatics/pyobo/pull/250
  • Update cruft by @cthoyt in https://github.com/biopragmatics/pyobo/pull/298
  • Cleanup for OFN by @cthoyt in https://github.com/biopragmatics/pyobo/pull/294
  • Don't emit builtin prefixes in OBO by @cthoyt in https://github.com/biopragmatics/pyobo/pull/296
  • Simplify CURIE passing in OFN by @cthoyt in https://github.com/biopragmatics/pyobo/pull/300
  • Add autogenerated annotation by @cthoyt in https://github.com/biopragmatics/pyobo/pull/299
  • Additional improvements for OFN output by @cthoyt in https://github.com/biopragmatics/pyobo/pull/301
  • Improve sorting by @cthoyt in https://github.com/biopragmatics/pyobo/pull/302
  • Add SIGNOR by @cthoyt in https://github.com/biopragmatics/pyobo/pull/303
  • Reorganize sources by @cthoyt in https://github.com/biopragmatics/pyobo/pull/305
  • Add UMLS STY by @cthoyt in https://github.com/biopragmatics/pyobo/pull/306
  • Update stanza types by @cthoyt in https://github.com/biopragmatics/pyobo/pull/308
  • Add append contributor shortcut by @cthoyt in https://github.com/biopragmatics/pyobo/pull/309
  • Add ClinicalTrials.gov source by @cthoyt in https://github.com/biopragmatics/pyobo/pull/307
  • Add source: ChEMBL Target by @cthoyt in https://github.com/biopragmatics/pyobo/pull/311
  • Add flag for turning off caching by @cthoyt in https://github.com/biopragmatics/pyobo/pull/313
  • Fix obonet caching by @cthoyt in https://github.com/biopragmatics/pyobo/pull/314
  • Use tqdm and cache flags everywhere by @cthoyt in https://github.com/biopragmatics/pyobo/pull/315
  • Refactor API code by @cthoyt in https://github.com/biopragmatics/pyobo/pull/312
  • Refactor reference passing by @cthoyt in https://github.com/biopragmatics/pyobo/pull/316
  • Add NotRequired annotations to typed dicts by @cthoyt in https://github.com/biopragmatics/pyobo/pull/319
  • Add URIs to provenance lists by @cthoyt in https://github.com/biopragmatics/pyobo/pull/318
  • Update interface for Stanza.annoate_literal by @cthoyt in https://github.com/biopragmatics/pyobo/pull/325
  • Remove unnecessary definition provenance list by @cthoyt in https://github.com/biopragmatics/pyobo/pull/327
  • Correctly handle unspecified synonym scope by @cthoyt in https://github.com/biopragmatics/pyobo/pull/328
  • Add language support to synonyms and literal property annotations by @cthoyt in https://github.com/biopragmatics/pyobo/pull/324
  • Add ROR organization classifications by @cthoyt in https://github.com/biopragmatics/pyobo/pull/326
  • Add PharmGKB sources by @cthoyt in https://github.com/biopragmatics/pyobo/pull/304
  • Update column for species in GTDB source by @jplfaria in https://github.com/biopragmatics/pyobo/pull/331
  • Update type hints for new beautifulsoup4 by @cthoyt in https://github.com/biopragmatics/pyobo/pull/335
  • Improve IDSPACES for sources by @cthoyt in https://github.com/biopragmatics/pyobo/pull/334
  • Improve synonym export by @cthoyt in https://github.com/biopragmatics/pyobo/pull/329
  • Handle datetimes and creation_date by @cthoyt in https://github.com/biopragmatics/pyobo/pull/320
  • Handle annotation objects with superfluous datatypes by @cthoyt in https://github.com/biopragmatics/pyobo/pull/339
  • Update date parsing by @cthoyt in https://github.com/biopragmatics/pyobo/pull/340
  • Refactor pyobo.Reference by @cthoyt in https://github.com/biopragmatics/pyobo/pull/341
  • Improve error handling in reader by @cthoyt in https://github.com/biopragmatics/pyobo/pull/342
  • Automatically upgrade lowercase synonym specificities by @cthoyt in https://github.com/biopragmatics/pyobo/pull/321
  • Add prefix summarization by @cthoyt in https://github.com/biopragmatics/pyobo/pull/337
  • Update URI parsing by @cthoyt in https://github.com/biopragmatics/pyobo/pull/344
  • Update ICD utilities by @cthoyt in https://github.com/biopragmatics/pyobo/pull/338
  • Reorganize NER code by @cthoyt in https://github.com/biopragmatics/pyobo/pull/345
  • Switch to SSSLM by @cthoyt in https://github.com/biopragmatics/pyobo/pull/346
  • Switch hierarchy and name API to return references by @cthoyt in https://github.com/biopragmatics/pyobo/pull/347
  • Update EC tests by @cthoyt in https://github.com/biopragmatics/pyobo/pull/351
  • Improve iteration over stanzas by @cthoyt in https://github.com/biopragmatics/pyobo/pull/353
  • Cleanup reference classes and parsing by @cthoyt in https://github.com/biopragmatics/pyobo/pull/350
  • Additional OBO reader refactoring by @cthoyt in https://github.com/biopragmatics/pyobo/pull/355
  • Cleanup docs by @cthoyt in https://github.com/biopragmatics/pyobo/pull/356
  • Implement comments in xrefs by @cthoyt in https://github.com/biopragmatics/pyobo/pull/357
  • Concatenate multiple DE lines. by @cmungall in https://github.com/biopragmatics/pyobo/pull/361
  • Add source annotation to EC by @cthoyt in https://github.com/biopragmatics/pyobo/pull/362
  • Adding reactions as definitions. by @cmungall in https://github.com/biopragmatics/pyobo/pull/363
  • Streamline cache path generation by @cthoyt in https://github.com/biopragmatics/pyobo/pull/365
  • Update sources by @cthoyt in https://github.com/biopragmatics/pyobo/pull/366
  • Turn off strict parsing by default by @cthoyt in https://github.com/biopragmatics/pyobo/pull/367
  • Remove xref plugins by @cthoyt in https://github.com/biopragmatics/pyobo/pull/371
  • Update cruft by @cthoyt in https://github.com/biopragmatics/pyobo/pull/372
  • Update reference validation and bioontologies by @cthoyt in https://github.com/biopragmatics/pyobo/pull/374
  • Make underlying identifier parsing functions not strict by default by @cthoyt in https://github.com/biopragmatics/pyobo/pull/379
  • Update ChEMBL target processor by @cthoyt in https://github.com/biopragmatics/pyobo/pull/378
  • Skip ad-hoc bases by @cthoyt in https://github.com/biopragmatics/pyobo/pull/377
  • Don't cache literal mappings in tests by @cthoyt in https://github.com/biopragmatics/pyobo/pull/381
  • Reimplement getting xrefs by @cthoyt in https://github.com/biopragmatics/pyobo/pull/380
  • Update hierarchy API by @cthoyt in https://github.com/biopragmatics/pyobo/pull/376
  • Switch to normalized references in more places by @cthoyt in https://github.com/biopragmatics/pyobo/pull/382
  • Address identifier validation issues by @cthoyt in https://github.com/biopragmatics/pyobo/pull/385
  • Update BiGG Metabolite source by @cthoyt in https://github.com/biopragmatics/pyobo/pull/387
  • Further BiGG Metabolite updates by @cthoyt in https://github.com/biopragmatics/pyobo/pull/388
  • Refactor CURIE/URI string preprocessing by @cthoyt in https://github.com/biopragmatics/pyobo/pull/390
  • Refactor identifier utils by @cthoyt in https://github.com/biopragmatics/pyobo/pull/391
  • Remove trailing slash from URLs by @cthoyt in https://github.com/biopragmatics/pyobo/pull/393
  • Add write_edges() function to ontology by @cthoyt in https://github.com/biopragmatics/pyobo/pull/394
  • Remove deprecated grounding code by @cthoyt in https://github.com/biopragmatics/pyobo/pull/392

New Contributors

  • @jplfaria made their first contribution in https://github.com/biopragmatics/pyobo/pull/234
  • @samuelbunga made their first contribution in https://github.com/biopragmatics/pyobo/pull/124
  • @cmungall made their first contribution in https://github.com/biopragmatics/pyobo/pull/361

Full Changelog: https://github.com/biopragmatics/pyobo/compare/v0.11.1...v0.12.0

- Python
Published by cthoyt about 1 year ago

https://github.com/biopragmatics/pyobo - v0.11.2

Full Changelog: https://github.com/biopragmatics/pyobo/compare/v0.11.1...v0.11.2

This PR adds requests-ftp as an explicit requirement to address #265

- Python
Published by cthoyt over 1 year ago

https://github.com/biopragmatics/pyobo - v0.11.1

What's Changed

  • Update sources for OBO database ingest by @cthoyt in https://github.com/biopragmatics/pyobo/pull/197
  • Use internal writer for OBO Graphs by @cthoyt in https://github.com/biopragmatics/pyobo/pull/198
  • Cache SO names by @cthoyt in https://github.com/biopragmatics/pyobo/pull/199
  • Improve model validation code by @cthoyt in https://github.com/biopragmatics/pyobo/pull/200
  • Add global switch for turning on ID checks by @cthoyt in https://github.com/biopragmatics/pyobo/pull/201

Full Changelog: https://github.com/biopragmatics/pyobo/compare/v0.11.0...v0.11.1

- Python
Published by cthoyt over 1 year ago

https://github.com/biopragmatics/pyobo - v0.11.0

What's Changed

  • Fix version pins by @nanglo123 in https://github.com/biopragmatics/pyobo/pull/192
  • Clean up by @cthoyt in https://github.com/biopragmatics/pyobo/pull/195
  • Use cookecutter-snekpack and bump to v0.11 by @cthoyt in https://github.com/biopragmatics/pyobo/pull/196

Version 0.11+ will only support Pydantic 2.

Full Changelog: https://github.com/biopragmatics/pyobo/compare/v0.10.12...v0.11.0

- Python
Published by cthoyt over 1 year ago

https://github.com/biopragmatics/pyobo - v0.10.12

What's Changed

  • Fix URL for rgd by @kkaris in https://github.com/biopragmatics/pyobo/pull/188
  • Enable use of enviornmental variable version pin dictionary by @nanglo123 in https://github.com/biopragmatics/pyobo/pull/189
  • Minor updates by @cthoyt in https://github.com/biopragmatics/pyobo/pull/193

New Contributors

  • @kkaris made their first contribution in https://github.com/biopragmatics/pyobo/pull/188
  • @nanglo123 made their first contribution in https://github.com/biopragmatics/pyobo/pull/189

Full Changelog: https://github.com/biopragmatics/pyobo/compare/v0.10.11...v0.10.12

- Python
Published by cthoyt over 1 year ago

https://github.com/biopragmatics/pyobo - v0.10.11

What's Changed

  • Add version keyword to all lookup functions by @cthoyt in https://github.com/biopragmatics/pyobo/pull/184

Full Changelog: https://github.com/biopragmatics/pyobo/compare/v0.10.10...v0.10.11

- Python
Published by cthoyt about 2 years ago

https://github.com/biopragmatics/pyobo - v0.10.10

What's Changed

  • Enable passing version to name getter by @cthoyt in https://github.com/biopragmatics/pyobo/pull/181
  • Track obsoletions in EC by @cthoyt in https://github.com/biopragmatics/pyobo/pull/182

Full Changelog: https://github.com/biopragmatics/pyobo/compare/v0.10.9...v0.10.10

- Python
Published by cthoyt about 2 years ago

https://github.com/biopragmatics/pyobo - v0.10.9

What's Changed

  • Extend UniProt export by @cthoyt in https://github.com/biopragmatics/pyobo/pull/173
  • Add UMLS semantic types by @cthoyt in https://github.com/biopragmatics/pyobo/pull/175
  • Add new sources for CiVIC Gene and OMIM Phenotypic series by @cthoyt in https://github.com/biopragmatics/pyobo/pull/176
  • other minor fixes

Full Changelog: https://github.com/biopragmatics/pyobo/compare/v0.10.8...v0.10.9

- Python
Published by cthoyt about 2 years ago

https://github.com/biopragmatics/pyobo - v0.10.8

What's Changed

  • Improve Rhea import by @cthoyt in https://github.com/biopragmatics/pyobo/pull/168
  • Handle CVX obsolete/replaced/placeholder entries by @cthoyt in https://github.com/biopragmatics/pyobo/pull/171

Full Changelog: https://github.com/biopragmatics/pyobo/compare/v0.10.7...v0.10.8

- Python
Published by cthoyt about 2 years ago

https://github.com/biopragmatics/pyobo - v0.10.7

What's Changed

  • Update synonym parsing to handle OMO CURIEs by @cthoyt in https://github.com/pyobo/pyobo/pull/166
  • handle missing hierarchy in geonames processor
  • improve handling of xrefs in ComplexPortal
  • Update EC, ComplexPortal, NPASS, and other resources
  • FIx the way definition sources get propogated
  • Add inverse property writing in OBO flat file export

Full Changelog: https://github.com/pyobo/pyobo/compare/v0.10.6...v0.10.7

- Python
Published by cthoyt over 2 years ago

https://github.com/biopragmatics/pyobo - v0.10.6

What's Changed

  • Use preferred prefixes when outputting OBO flat files by @cthoyt in https://github.com/pyobo/pyobo/pull/164

Full Changelog: https://github.com/pyobo/pyobo/compare/v0.10.5...v0.10.6

- Python
Published by cthoyt over 2 years ago

https://github.com/biopragmatics/pyobo - v0.10.5

Full Changelog: https://github.com/pyobo/pyobo/compare/v0.10.4...v0.10.5

- Python
Published by cthoyt over 2 years ago

https://github.com/biopragmatics/pyobo - v0.10.4

Full Changelog: https://github.com/pyobo/pyobo/compare/v0.10.3...v0.10.4

- Python
Published by cthoyt over 2 years ago

https://github.com/biopragmatics/pyobo -

- Python
Published by cthoyt over 2 years ago

https://github.com/biopragmatics/pyobo - v0.10.2

What's Changed

  • Enforce all references are standardized by @cthoyt in https://github.com/pyobo/pyobo/pull/156

Full Changelog: https://github.com/pyobo/pyobo/compare/v0.10.1...v0.10.2

- Python
Published by cthoyt almost 3 years ago

https://github.com/biopragmatics/pyobo - v0.10.1

What's Changed

  • Update MeSH import for 2023+ data by @hrshdhgd in https://github.com/pyobo/pyobo/pull/151
  • Make adding names to SSSOM optional by @cthoyt in https://github.com/pyobo/pyobo/pull/154

New Contributors

  • @hrshdhgd made their first contribution in https://github.com/pyobo/pyobo/pull/151

Full Changelog: https://github.com/pyobo/pyobo/compare/v0.10.0...v0.10.1

- Python
Published by cthoyt almost 3 years ago

https://github.com/biopragmatics/pyobo - v0.10.0

What's Changed

  • Add pydantic1/2 compatibility by @cthoyt in https://github.com/pyobo/pyobo/pull/152

Full Changelog: https://github.com/pyobo/pyobo/compare/v0.9.2...v0.10.0

- Python
Published by cthoyt almost 3 years ago

https://github.com/biopragmatics/pyobo - v0.8.14

What's Changed

  • Update UniProt download by @cthoyt in https://github.com/pyobo/pyobo/pull/149

Full Changelog: https://github.com/pyobo/pyobo/compare/v0.8.13...v0.8.14

- Python
Published by cthoyt about 3 years ago

https://github.com/biopragmatics/pyobo - v0.8.13

What's Changed

  • Update sources by @cthoyt in https://github.com/pyobo/pyobo/pull/147

Full Changelog: https://github.com/pyobo/pyobo/compare/v0.8.12...v0.8.13

- Python
Published by cthoyt about 3 years ago

https://github.com/biopragmatics/pyobo - v0.8.7

What's Changed

  • Enable specifying version for sources by @cthoyt in https://github.com/pyobo/pyobo/pull/137

Full Changelog: https://github.com/pyobo/pyobo/compare/v0.8.6...v0.8.7

- Python
Published by cthoyt over 3 years ago

https://github.com/biopragmatics/pyobo - v0.8.6

Full Changelog: https://github.com/pyobo/pyobo/compare/v0.8.5...v0.8.6

- Python
Published by cthoyt over 3 years ago

https://github.com/biopragmatics/pyobo - v0.8.5

What's Changed

  • Upgrade python by @cthoyt in https://github.com/pyobo/pyobo/pull/134
  • Update synonyms handling by @cthoyt in https://github.com/pyobo/pyobo/pull/138

Full Changelog: https://github.com/pyobo/pyobo/compare/v0.8.4...v0.8.5

- Python
Published by cthoyt over 3 years ago

https://github.com/biopragmatics/pyobo - v0.8.4

Full Changelog: https://github.com/pyobo/pyobo/compare/v0.8.3...v0.8.4

- Python
Published by cthoyt over 3 years ago

https://github.com/biopragmatics/pyobo - v0.8.1

Full Changelog: https://github.com/pyobo/pyobo/compare/v0.8.0...v0.8.1

Fixes Wikidata download issue

- Python
Published by cthoyt almost 4 years ago

https://github.com/biopragmatics/pyobo - v0.8.0

What's Changed

  • Update package configuration by @cthoyt in https://github.com/pyobo/pyobo/pull/132
  • Make sure identifiers in source column are normalized by @cthoyt in https://github.com/pyobo/pyobo/pull/122

Full Changelog: https://github.com/pyobo/pyobo/compare/v0.7.0...v0.8.0

- Python
Published by cthoyt almost 4 years ago

https://github.com/biopragmatics/pyobo - v0.7.0

What's Changed

  • Add Antibody Registry by @cthoyt in https://github.com/pyobo/pyobo/pull/121
  • Enable passing a custom Gilda grounder class by @cthoyt in https://github.com/pyobo/pyobo/pull/120
  • Externalize ontology loading from OBO clas by @cthoyt in https://github.com/pyobo/pyobo/pull/127
  • Require static typing by @cthoyt in https://github.com/pyobo/pyobo/pull/130
  • Update version handling by @cthoyt in https://github.com/pyobo/pyobo/pull/131
  • Switch to class-based interface by @cthoyt in https://github.com/pyobo/pyobo/pull/129

Full Changelog: https://github.com/pyobo/pyobo/compare/v0.6.5...v0.7.0

- Python
Published by cthoyt almost 4 years ago

https://github.com/biopragmatics/pyobo -

  • remove code that is now in biolookup
  • add species lookup in CLI
  • add species table generation

- Python
Published by cthoyt almost 5 years ago

https://github.com/biopragmatics/pyobo -

Code cleanup and name change from bioresolver to biolookup

- Python
Published by cthoyt almost 5 years ago

https://github.com/biopragmatics/pyobo -

  • Add SLM
  • Use chembl_downlader for ChEBML data acquisition
  • Make MeSH get latest data\
  • Fix interpro processing (#116, thanks @bgyori)

- Python
Published by cthoyt almost 5 years ago

https://github.com/biopragmatics/pyobo -

  • Improve code for working with Gilda
  • Add new sources (ccle, depmap, 4 selventa resources)

- Python
Published by cthoyt almost 5 years ago

https://github.com/biopragmatics/pyobo -

Update based on bioregistry and bioversions

- Python
Published by cthoyt almost 5 years ago

https://github.com/biopragmatics/pyobo -

Lots of updates to build pipeline and usage of the bioregistry

- Python
Published by cthoyt about 5 years ago

https://github.com/biopragmatics/pyobo -

  • Add getter for property pyobo.get_property
  • Update database build
  • Add Rhea
  • Add automated upload to zenodo

- Python
Published by cthoyt over 5 years ago

https://github.com/biopragmatics/pyobo -

- Python
Published by cthoyt over 5 years ago

https://github.com/biopragmatics/pyobo -

  • Add species lookup
  • Better handling of versioned data
  • Add orthologous relation
  • More strict usage of the bioregistry

- Python
Published by cthoyt over 5 years ago

https://github.com/biopragmatics/pyobo -

- Python
Published by cthoyt over 5 years ago

https://github.com/biopragmatics/pyobo -

- Python
Published by cthoyt over 5 years ago

https://github.com/biopragmatics/pyobo -

Fix typo in parsing of FamPlex equivalences

- Python
Published by cthoyt over 5 years ago

https://github.com/biopragmatics/pyobo -

- Python
Published by cthoyt over 5 years ago

https://github.com/biopragmatics/pyobo -

- Python
Published by cthoyt over 5 years ago

https://github.com/biopragmatics/pyobo -

This time, with mocks and better protmapper integration

- Python
Published by cthoyt over 5 years ago

https://github.com/biopragmatics/pyobo -

- Python
Published by cthoyt over 5 years ago

https://github.com/biopragmatics/pyobo -

- Python
Published by cthoyt about 6 years ago

https://github.com/biopragmatics/pyobo -

- Python
Published by cthoyt about 6 years ago

https://github.com/biopragmatics/pyobo -

- Python
Published by cthoyt about 6 years ago

https://github.com/biopragmatics/pyobo -

- Python
Published by cthoyt about 6 years ago

https://github.com/biopragmatics/pyobo -

- Python
Published by cthoyt about 6 years ago

https://github.com/biopragmatics/pyobo -

- Python
Published by cthoyt about 6 years ago

https://github.com/biopragmatics/pyobo -

- Python
Published by cthoyt about 6 years ago

https://github.com/biopragmatics/pyobo -

- Python
Published by cthoyt about 6 years ago

https://github.com/biopragmatics/pyobo -

- Python
Published by cthoyt about 6 years ago

https://github.com/biopragmatics/pyobo -

  • Fix bug in xref getter
  • Add more default TypeDefs
  • Improve support for explicitly versioned data
  • Add ComplexPortal source

- Python
Published by cthoyt about 6 years ago

https://github.com/biopragmatics/pyobo -

- Python
Published by cthoyt about 6 years ago

https://github.com/biopragmatics/pyobo -

- Python
Published by cthoyt about 6 years ago

https://github.com/biopragmatics/pyobo -

- Python
Published by cthoyt about 6 years ago

https://github.com/biopragmatics/pyobo -

- Python
Published by cthoyt over 6 years ago

https://github.com/biopragmatics/pyobo - Initial release

Added initial (incomplete) data structures for representing and outputting OBO. So far, it covers the use cases for CONSO

- Python
Published by cthoyt almost 7 years ago