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

https://github.com/biopragmatics/biomappings - v0.4.0

What's Changed

  • Curate CVX mismatches by @cthoyt in https://github.com/biopragmatics/biomappings/pull/162
  • Curated some MONDO-MeSH mappings (sumir) by @sumirp in https://github.com/biopragmatics/biomappings/pull/152
  • Improve docs about data model for predictions by @cthoyt in https://github.com/biopragmatics/biomappings/pull/163
  • Update webapp footer by @bgyori in https://github.com/biopragmatics/biomappings/pull/164
  • Set text-nowrap for -B- and -N- columns by @kkaris in https://github.com/biopragmatics/biomappings/pull/165
  • More ChEBI-MeSH curations by @bgyori in https://github.com/biopragmatics/biomappings/pull/166
  • Update MeSH predictions and curations by @bgyori in https://github.com/biopragmatics/biomappings/pull/168
  • Update package to use snekpack by @cthoyt in https://github.com/biopragmatics/biomappings/pull/171
  • Update Readme by @KrishnaTO in https://github.com/biopragmatics/biomappings/pull/174
  • Curated 10 mappings (sumirpandit) by @sumirp in https://github.com/biopragmatics/biomappings/pull/169
  • Switch to using Bioregistry standard instead of MIRIAM by @cthoyt in https://github.com/biopragmatics/biomappings/pull/190
  • Update PyOBO usage by @cthoyt in https://github.com/biopragmatics/biomappings/pull/191
  • Switch source curation files to SSSOM format by @cthoyt in https://github.com/biopragmatics/biomappings/pull/192
  • Update types and type hints by @cthoyt in https://github.com/biopragmatics/biomappings/pull/195
  • Switch to using Pydantic models by @cthoyt in https://github.com/biopragmatics/biomappings/pull/196
  • Add stripping whitespace to linting by @cthoyt in https://github.com/biopragmatics/biomappings/pull/194
  • Fix summary and add some curations by @cthoyt in https://github.com/biopragmatics/biomappings/pull/199

New Contributors

  • @kkaris made their first contribution in https://github.com/biopragmatics/biomappings/pull/165
  • @KrishnaTO made their first contribution in https://github.com/biopragmatics/biomappings/pull/174

Full Changelog: https://github.com/biopragmatics/biomappings/compare/v0.3.7...v0.4.0

- Jupyter Notebook
Published by cthoyt 11 months ago

https://github.com/biopragmatics/biomappings - v0.3.7

What's Changed

  • Enforce using CURIEs for all relationships by @cthoyt in https://github.com/biopragmatics/biomappings/pull/123
  • Ensure SSSOM file is valid by @cthoyt in https://github.com/biopragmatics/biomappings/pull/155
  • Use preferred prefixes in SSSOM by @cthoyt in https://github.com/biopragmatics/biomappings/pull/157
  • Add broad/narrow curation to interface by @cthoyt in https://github.com/biopragmatics/biomappings/pull/158
  • Add custom predictions and custom deployment tutorials by @cthoyt in https://github.com/biopragmatics/biomappings/pull/160
  • Add VO-DrugBank predictions and curations by @cthoyt in https://github.com/biopragmatics/biomappings/pull/159

Full Changelog: https://github.com/biopragmatics/biomappings/compare/v0.3.6...v0.3.7

- Jupyter Notebook
Published by cthoyt over 2 years ago

https://github.com/biopragmatics/biomappings - v0.3.6

What's Changed

  • Add summary page button by @cthoyt in https://github.com/biopragmatics/biomappings/pull/145
  • Improve trackability of committer by @cthoyt in https://github.com/biopragmatics/biomappings/pull/148
  • Update testing with py38 by @cthoyt in https://github.com/biopragmatics/biomappings/pull/150
  • Add generic contribution workflow to OBO flat files by @cthoyt in https://github.com/biopragmatics/biomappings/pull/149
  • CVX and MeSH mappings by @cthoyt in https://github.com/biopragmatics/biomappings/pull/147
  • Curated 1 mapping (sumir) by @sumirp in https://github.com/biopragmatics/biomappings/pull/151

New Contributors

  • @sumirp made their first contribution in https://github.com/biopragmatics/biomappings/pull/151

Full Changelog: https://github.com/biopragmatics/biomappings/compare/v0.3.5...v0.3.6

- Jupyter Notebook
Published by cthoyt over 2 years ago

https://github.com/biopragmatics/biomappings - v0.3.5

What's Changed

  • Update linting on predictions by @cthoyt in https://github.com/biopragmatics/biomappings/pull/144

Full Changelog: https://github.com/biopragmatics/biomappings/compare/v0.3.4...v0.3.5

- Jupyter Notebook
Published by cthoyt over 2 years ago

https://github.com/biopragmatics/biomappings - v0.3.4

What's Changed

  • Override MIRIAM OBI pattern by @cthoyt in https://github.com/biopragmatics/biomappings/pull/143

Full Changelog: https://github.com/biopragmatics/biomappings/compare/v0.3.3...v0.3.4

- Jupyter Notebook
Published by cthoyt over 2 years ago

https://github.com/biopragmatics/biomappings - v0.3.3

What's Changed

  • Improve redundancy filtering by @cthoyt in https://github.com/biopragmatics/biomappings/pull/141
  • Make tests reusable by @cthoyt in https://github.com/biopragmatics/biomappings/pull/142

Full Changelog: https://github.com/biopragmatics/biomappings/compare/v0.3.2...v0.3.3

- Jupyter Notebook
Published by cthoyt over 2 years ago

https://github.com/biopragmatics/biomappings - v0.3.2

What's Changed

  • Add UBERON-BTO predictions by @bgyori in https://github.com/biopragmatics/biomappings/pull/129
  • Add custom predictions flag in web app runner by @cthoyt in https://github.com/biopragmatics/biomappings/pull/130
  • Fix gilda prediction workflow by @cthoyt in https://github.com/biopragmatics/biomappings/pull/131
  • Add more curations by @cthoyt in https://github.com/biopragmatics/biomappings/pull/132
  • Add CLO processing notebook by @cthoyt in https://github.com/biopragmatics/biomappings/pull/133
  • Update state handling by @cthoyt in https://github.com/biopragmatics/biomappings/pull/134
  • Additional cell, cell line, and tissue curations by @cthoyt in https://github.com/biopragmatics/biomappings/pull/135
  • Generate MAxO-MeSH predictions by @cthoyt in https://github.com/biopragmatics/biomappings/pull/137
  • Add negative mappings to SSSOM output by @cthoyt in https://github.com/biopragmatics/biomappings/pull/138
  • Enable custom curation files by @cthoyt in https://github.com/biopragmatics/biomappings/pull/140

Full Changelog: https://github.com/biopragmatics/biomappings/compare/v0.3.1...v0.3.2

- Jupyter Notebook
Published by cthoyt almost 3 years ago

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

- Jupyter Notebook
Published by cthoyt almost 3 years ago

https://github.com/biopragmatics/biomappings - v0.3.0 - Publication revision

This release corresponds to the changes that go with the re-submission of the biomappings paper.

What's Changed

  • Assess curation precision by @cthoyt in https://github.com/biopragmatics/biomappings/pull/113
  • Add sort by confidence to web app by @cthoyt in https://github.com/biopragmatics/biomappings/pull/75
  • Add epidemiology curation by @cthoyt in https://github.com/biopragmatics/biomappings/pull/115
  • Cleanup and update by @cthoyt in https://github.com/biopragmatics/biomappings/pull/116
  • Improve prediction linting by @cthoyt in https://github.com/biopragmatics/biomappings/pull/118
  • Propagate metadata from predictions into curated files by @cthoyt in https://github.com/biopragmatics/biomappings/pull/117

Full Changelog: https://github.com/biopragmatics/biomappings/compare/v0.2.0...v0.3.0

- Jupyter Notebook
Published by cthoyt over 3 years ago

https://github.com/biopragmatics/biomappings - v0.2.0

This release prepares for the Biomappings paper submission (probably that no more curations are necessary before next release).

What's Changed

  • Add predictions and curations for MeSH-ChEBI equivalences by @bgyori in https://github.com/biopragmatics/biomappings/pull/70
  • Predict DOID mappings to UMLS, MeSH, and EFO by @cthoyt in https://github.com/biopragmatics/biomappings/pull/68
  • Add more specific script URL for predictions by @bgyori in https://github.com/biopragmatics/biomappings/pull/76
  • Assorted DOID and ChEBI curations by @cthoyt in https://github.com/biopragmatics/biomappings/pull/74
  • Add manually curated PubChem-MeSH mappings by @bgyori in https://github.com/biopragmatics/biomappings/pull/77
  • Remove DOID mappings where primary mappings exist by @bgyori in https://github.com/biopragmatics/biomappings/pull/79
  • Remove more redundant predictions and curate some DOID mappings by @bgyori in https://github.com/biopragmatics/biomappings/pull/80
  • More manual DOID-MeSH curation by @bgyori in https://github.com/biopragmatics/biomappings/pull/81
  • Add UBERON-MeSH mappings by @bgyori in https://github.com/biopragmatics/biomappings/pull/86
  • Generate and curate a new set of MESH-CHEBI mappings by @bgyori in https://github.com/biopragmatics/biomappings/pull/89
  • Predict and curate CL-MESH mappings by @bgyori in https://github.com/biopragmatics/biomappings/pull/91
  • Miscellaneous curation by @bgyori in https://github.com/biopragmatics/biomappings/pull/92
  • More curations by @bgyori in https://github.com/biopragmatics/biomappings/pull/93
  • Curate MONDO-MeSH mappings by @bgyori in https://github.com/biopragmatics/biomappings/pull/95
  • Add AGRO-AGROVOC mappings by @cthoyt in https://github.com/biopragmatics/biomappings/pull/83
  • Curate AGRO-AGROVOC-Mappings by @cthoyt in https://github.com/biopragmatics/biomappings/pull/97
  • Add predicted WikiPathways orthologs by @cthoyt in https://github.com/biopragmatics/biomappings/pull/59
  • Additional curation and updates for bioregistry by @cthoyt in https://github.com/biopragmatics/biomappings/pull/98
  • Improve interface by @cthoyt in https://github.com/biopragmatics/biomappings/pull/99
  • Update MONDO local unique identifiers by @cthoyt in https://github.com/biopragmatics/biomappings/pull/105
  • Curate additional DOID-MESH mappings and contribute to DOID by @bgyori in https://github.com/biopragmatics/biomappings/pull/104
  • Some MeSH curations by @bgyori in https://github.com/biopragmatics/biomappings/pull/107
  • Add hetionet duplication and value added notebooks by @cthoyt in https://github.com/biopragmatics/biomappings/pull/102
  • Add project governance documentation by @cthoyt in https://github.com/biopragmatics/biomappings/pull/106
  • Fill out project skeleton by @cthoyt in https://github.com/biopragmatics/biomappings/pull/108

Full Changelog: https://github.com/biopragmatics/biomappings/compare/v0.1.2...v0.2.0

- Jupyter Notebook
Published by cthoyt over 3 years ago

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

  • Improve curation interface
  • Add new tools for generating predictions from PyOBO/Gilda
  • Add additional curations for CCLE (thanks @ALHoyt)
  • Import ComPath
  • Add APICURON upload

- Jupyter Notebook
Published by cthoyt over 4 years ago

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

Fix picture in readme

- Jupyter Notebook
Published by cthoyt almost 5 years ago

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

  • Refactor gilda predictions pipeline
  • Add major curation of DOID-MeSH by @ALHoyt

- Jupyter Notebook
Published by cthoyt almost 5 years ago

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

- Jupyter Notebook
Published by cthoyt over 5 years ago

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

- Jupyter Notebook
Published by cthoyt over 5 years ago

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

- Jupyter Notebook
Published by cthoyt over 5 years ago

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

- Jupyter Notebook
Published by cthoyt over 5 years ago