obofoundry/cob issues and pull requests

#248 - Replace CARO IDs in cob-non-native OWL export

Issue - State: open - Opened by cmungall 12 months ago

#247 - Update COB release (nucleic acid / electron fix)

Pull Request - State: closed - Opened by matentzn about 1 year ago

#246 - Fix Electron / nucleic acid polymer label

Pull Request - State: closed - Opened by matentzn about 1 year ago

#245 - electron has extra bad label

Issue - State: closed - Opened by ddooley about 1 year ago - 1 comment

#244 - Release COB with COB ids + mappings, rather than with the mapped IDs

Issue - State: open - Opened by matentzn over 1 year ago - 33 comments

#243 - COB changes preferred labels of several ontologies

Issue - State: open - Opened by matentzn over 1 year ago - 4 comments

#242 - Consider linking from COB documentation page to recent Ontology Summit presentation

Issue - State: open - Opened by jamesaoverton over 1 year ago
Labels: good first issue, documentation

#241 - Upgrading FoodOn to work with COB as top-level

Issue - State: open - Opened by ddooley over 1 year ago - 1 comment

#240 - Is COB "action specification" supposed to be different from IAO term?

Issue - State: open - Opened by ddooley over 1 year ago

#239 - environmental process

Issue - State: open - Opened by masciam over 1 year ago - 2 comments

#238 - Proposed SOP: all NTR PRs where there exists at least one equivalent in OBO should be accompanied by a change in cob-to-external

Issue - State: open - Opened by cmungall over 1 year ago - 3 comments

#237 - Add CONTRIBUTING.md and COC

Pull Request - State: closed - Opened by matentzn over 1 year ago

#236 - Add term-metadata schema to COB

Issue - State: open - Opened by matentzn over 1 year ago - 3 comments

#235 - cob-edit.owl: OWL API 4.5.25 normalisation

Pull Request - State: closed - Opened by matentzn over 1 year ago

#234 - Fix BFO:immaterial entity

Pull Request - State: closed - Opened by matentzn over 1 year ago - 1 comment

#233 - COB immaterial entity has wrong BFO ID

Issue - State: closed - Opened by ddooley over 1 year ago - 1 comment

#232 - Added "device"

Pull Request - State: closed - Opened by ddooley almost 2 years ago - 6 comments

#231 - ID ranges for ddooley

Pull Request - State: closed - Opened by ddooley almost 2 years ago

#230 - COB Normalisation Release ODK 14

Pull Request - State: closed - Opened by matentzn almost 2 years ago

#229 - Avoid use of "inverse(Property)" expression in class expressions in favour of providing an inverse relation

Issue - State: open - Opened by matentzn almost 2 years ago - 1 comment

#228 - ODK 1.4 update

Pull Request - State: closed - Opened by matentzn almost 2 years ago

#227 - 404 for Bridging COB to OBO

Issue - State: closed - Opened by ashkotin almost 2 years ago

#226 - Add "disease or disorder" to COB

Pull Request - State: open - Opened by matentzn almost 2 years ago - 65 comments

#225 - Add "phenotype" to COB

Pull Request - State: open - Opened by matentzn almost 2 years ago - 5 comments

#224 - Policy around using COB identifiers vs other OBO Ontology identifiers

Issue - State: open - Opened by ddooley almost 2 years ago - 10 comments

#223 - drop executes property chain

Pull Request - State: open - Opened by wdduncan about 2 years ago

#222 - NTR device, replacing OBI device

Issue - State: closed - Opened by ddooley about 2 years ago - 6 comments

#221 - Making realizable a disjoint union of disposition and role.

Pull Request - State: open - Opened by cmungall about 2 years ago - 1 comment

#220 - not sure how a plan can be sibling of both disposition and role

Issue - State: open - Opened by wdduncan about 2 years ago - 6 comments

#219 - Express COB as a formal schema

Issue - State: open - Opened by cmungall about 2 years ago - 2 comments

#218 - Add a "characteristic attribute" and "characteristic value" class

Issue - State: open - Opened by cmungall about 2 years ago - 9 comments

#217 - drop executes property chain: realizes o concretizes

Issue - State: open - Opened by wdduncan about 2 years ago - 24 comments

#216 - Pin SSSOM version again

Pull Request - State: closed - Opened by matentzn about 2 years ago

#215 - COB Release 2 Nov

Pull Request - State: closed - Opened by matentzn about 2 years ago - 4 comments

#214 - Plan to effectively push COB forward

Issue - State: open - Opened by cmungall over 2 years ago - 1 comment

#213 - RO axioms that have domain/range constraints with BFO classes above the COB shoreline

Issue - State: open - Opened by cmungall over 2 years ago - 2 comments

#212 - do not pin sssom

Pull Request - State: closed - Opened by cmungall over 2 years ago - 1 comment

#211 - Eliminating ncbitaxon:root and instead bridging to true organism subclasses

Pull Request - State: closed - Opened by cmungall over 2 years ago

#210 - make release with exposure of organism class

Issue - State: open - Opened by wdduncan over 2 years ago - 7 comments

#209 - Align with allotrope

Issue - State: open - Opened by cmungall over 2 years ago - 1 comment

#208 - add exposure of organism class

Pull Request - State: closed - Opened by wdduncan over 2 years ago - 1 comment

#207 - Adding ID ranges to COB

Pull Request - State: closed - Opened by matentzn over 2 years ago - 4 comments

#206 - Does COB want to inherit "system" from RO?

Issue - State: open - Opened by ddooley over 2 years ago - 5 comments

#205 - Add list of contributors to cob-edit

Issue - State: open - Opened by cmungall over 2 years ago - 2 comments

#204 - NTR: organism part derivative

Issue - State: open - Opened by cmungall over 2 years ago - 8 comments

#203 - add documentation for adding terms

Issue - State: open - Opened by wdduncan over 2 years ago - 5 comments
Labels: documentation

#202 - Patch Release May 2

Pull Request - State: closed - Opened by matentzn over 2 years ago

#201 - Changing has quantity to data property

Pull Request - State: closed - Opened by matentzn over 2 years ago

#200 - 'has quantity' declared as both data property and object property in base file

Issue - State: closed - Opened by balhoff over 2 years ago

#199 - avoid external annotations in base file

Issue - State: open - Opened by balhoff over 2 years ago

#198 - ODK Migrate and IRI fixes

Pull Request - State: closed - Opened by matentzn over 2 years ago - 1 comment

#197 - problems with ontology IRIs

Issue - State: closed - Opened by balhoff over 2 years ago - 1 comment

#196 - PURL for cob-to-external broken

Issue - State: closed - Opened by cmungall over 2 years ago - 1 comment

#195 - Where should terms like "sample mass", "patient email address", "latitude", etc be placed in COB

Issue - State: open - Opened by cmungall over 2 years ago

#194 - Create LICENSE

Pull Request - State: closed - Opened by cthoyt almost 3 years ago

#193 - test-making-chebi-atom-equiv

Pull Request - State: open - Opened by cmungall almost 3 years ago

#192 - add exposure of organism class

Issue - State: closed - Opened by wdduncan almost 3 years ago - 41 comments
Labels: enhancement, ECTO

#191 - Incorrect ID for 'planned process' in cob-to-external

Issue - State: open - Opened by beckyjackson about 3 years ago - 1 comment

#190 - NTR: observing system

Issue - State: open - Opened by cmungall about 3 years ago - 10 comments

#189 - Adding mapping_set_id and match_type to SSSOM file

Pull Request - State: closed - Opened by matentzn about 3 years ago

#188 - Link NCIT branches to COB

Issue - State: open - Opened by diatomsRcool about 3 years ago

#187 - Add terms for specialized data type classes

Issue - State: open - Opened by wdduncan over 3 years ago - 1 comment

#186 - NTR: Gene Group

Issue - State: open - Opened by cthoyt over 3 years ago

#185 - COB alignment annotations (SSSOM) dont show up in release

Issue - State: open - Opened by matentzn over 3 years ago - 1 comment

#184 - Disjoints of upper level classes to detect inconsistencies

Issue - State: open - Opened by bpeters42 over 3 years ago

#183 - Update cob-edit.owl closes #182

Pull Request - State: closed - Opened by bpeters42 over 3 years ago

#182 - planned process under realizable

Issue - State: closed - Opened by bpeters42 over 3 years ago - 2 comments

#181 - Issue running `sh run.sh make`

Issue - State: open - Opened by cthoyt over 3 years ago - 1 comment

#180 - Makefile: create tmpdir if not exist, add QC check

Pull Request - State: closed - Opened by matentzn over 3 years ago

#179 - Add gene and related entities from SO

Pull Request - State: open - Opened by cmungall over 3 years ago - 4 comments

#178 - usage docs

Pull Request - State: closed - Opened by cmungall over 3 years ago

#177 - Adding pandasql to dependencies

Pull Request - State: closed - Opened by matentzn over 3 years ago

#176 - Issue running `sh run.sh make main_test`

Issue - State: closed - Opened by cthoyt over 3 years ago - 5 comments

#175 - Update to ODK docs

Pull Request - State: closed - Opened by matentzn over 3 years ago

#174 - Issue running `make`: No rule to make target `cob-edit.owl'

Issue - State: closed - Opened by cthoyt over 3 years ago - 2 comments

#173 - Add superclass mapping from COB characteristic to ChEBI role

Pull Request - State: closed - Opened by cthoyt over 3 years ago - 5 comments

#172 - new release, rewired is not main

Pull Request - State: closed - Opened by cmungall over 3 years ago

#171 - rewire

Pull Request - State: closed - Opened by cmungall over 3 years ago

#170 - new site

Pull Request - State: closed - Opened by cmungall over 3 years ago

#169 - Mappings for ChEBI has role property and chemical role class

Issue - State: closed - Opened by cthoyt over 3 years ago

#168 - Cant serialise COB in OBO format

Issue - State: open - Opened by matentzn over 3 years ago - 8 comments

#167 - COB ODK setup

Pull Request - State: closed - Opened by matentzn over 3 years ago - 3 comments

#166 - Migrate to sssom 0.3.2 and re-run

Pull Request - State: closed - Opened by matentzn over 3 years ago - 2 comments

#165 - COB rewired 147

Pull Request - State: closed - Opened by cmungall over 3 years ago - 2 comments

#164 - Remove quality

Pull Request - State: closed - Opened by beckyjackson over 3 years ago

#163 - Convert this repository to ODK format

Issue - State: closed - Opened by jamesaoverton over 3 years ago

#161 - Have a mapping file to non-OBO ontologies/vocabularies in SSSOM

Issue - State: open - Opened by StroemPhi over 3 years ago - 6 comments

#159 - Make organisation (COB_0000025) a GDC?

Issue - State: closed - Opened by StroemPhi over 3 years ago - 13 comments

#156 - NTRs: behavior and human activity

Issue - State: open - Opened by cmungall almost 4 years ago - 14 comments

#151 - false positive orphans when using base file

Issue - State: closed - Opened by cmungall almost 4 years ago - 3 comments

#148 - Change IRI of based_on

Issue - State: open - Opened by matentzn about 4 years ago - 1 comment

#147 - Generate an ontology that is COB rewired to OBO classes

Issue - State: open - Opened by cmungall over 4 years ago - 5 comments

#146 - Process start and end time/date

Issue - State: open - Opened by johnwjudkins over 4 years ago - 13 comments

#133 - Using sssom-py instead of tsv2rdf.pl

Issue - State: closed - Opened by matentzn over 4 years ago - 2 comments
Labels: technical

#124 - Where to place "phenotypic quality" (PATO)

Issue - State: closed - Opened by matentzn over 4 years ago - 7 comments

#116 - Remove quality for COB

Issue - State: closed - Opened by wdduncan over 4 years ago - 3 comments
Labels: COB 2020 Workshop

#54 - Decide on prefix and register with OBO

Issue - State: closed - Opened by cmungall about 5 years ago - 33 comments
Labels: technical

#53 - Add process profile to OBO-core

Issue - State: closed - Opened by wdduncan about 5 years ago - 26 comments

#52 - Considerations for SO terms

Issue - State: open - Opened by beckyjackson about 5 years ago - 5 comments
Labels: SO

#51 - NTR: processual stage/phase (e.g cell cycle stage, old age, holocene, daylight hours)

Issue - State: open - Opened by cmungall about 5 years ago
Labels: UBERON, GO

GitHub / obofoundry/cob issues and pull requests