biolink/biolink-model issues and pull requests

#1536 - moves specialization qualifiers & disease context qualifier up to disease or phenotypic feature association

Pull Request - State: open - Opened by kevinschaper 6 days ago

#1535 - Add species context qualifier to macromolecular machine association mixin

Pull Request - State: closed - Opened by kevinschaper 9 days ago

#1534 - add subject/object specialization qualifier to help represent extensions in MAXO and GO-CAM

Pull Request - State: closed - Opened by sierra-moxon 10 days ago

#1533 - Move disease_context_qualifier up to a higher level mixin

Pull Request - State: closed - Opened by kevinschaper 13 days ago

#1532 - Predicate inverses & tests

Pull Request - State: closed - Opened by sierra-moxon 20 days ago

#1531 - Add ICD11 as a prefix for Disease

Issue - State: open - Opened by gaurav 27 days ago

#1530 - ready the repo for release

Pull Request - State: closed - Opened by sierra-moxon about 1 month ago

#1529 - Add disease context qualifier (to the right place this time)

Pull Request - State: closed - Opened by kevinschaper about 1 month ago

#1528 - Remove if absent annotations causing downstream issues in python dataclasses

Pull Request - State: closed - Opened by sierra-moxon about 1 month ago

#1527 - fix gen-pydantic command

Pull Request - State: closed - Opened by sierra-moxon about 1 month ago

#1526 - Update biolink-model.yaml for CTKP requirements

Pull Request - State: closed - Opened by mbrush about 1 month ago

#1525 - response to predicate additions

Pull Request - State: open - Opened by sierra-moxon about 2 months ago

#1524 - Add disease context qualifier and make it available only to phenotype associations (initially, at least)

Pull Request - State: closed - Opened by kevinschaper 2 months ago

#1523 - Add medical action above treatment, plus action to disease & action to phenotype associations

Pull Request - State: closed - Opened by kevinschaper 2 months ago - 3 comments

#1522 - Update biolink-model.yaml - minor update to 'treats' def

Pull Request - State: closed - Opened by mbrush 3 months ago

#1521 - 4.2.2 release

Pull Request - State: closed - Opened by sierra-moxon 4 months ago

#1520 - Bump setuptools from 69.0.2 to 70.0.0

Pull Request - State: closed - Opened by dependabot[bot] 4 months ago
Labels: dependencies

#1519 - Bump zipp from 3.17.0 to 3.19.1

Pull Request - State: closed - Opened by dependabot[bot] 4 months ago
Labels: dependencies

#1518 - Bump certifi from 2023.11.17 to 2024.7.4

Pull Request - State: closed - Opened by dependabot[bot] 4 months ago
Labels: dependencies

#1517 - Add GeneticCode as an attribute, and a has_genetic_code predicate

Issue - State: open - Opened by cmungall 5 months ago

#1516 - prefixes in use not in biolink prefixmap

Issue - State: open - Opened by sierra-moxon 5 months ago

#1515 - add max research phase enum values

Issue - State: open - Opened by sierra-moxon 5 months ago
Labels: help-desk

#1514 - Add info to association qualifiers describing which part of the statement they apply to

Issue - State: open - Opened by Woozl 5 months ago - 2 comments
Labels: question, working-group/ROBOKOP

#1513 - Bump urllib3 from 2.1.0 to 2.2.2

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago
Labels: dependencies

#1512 - fix: flip domain/range for top-level "treats" predicates

Pull Request - State: closed - Opened by colleenXu 5 months ago

#1511 - Is the domain of 'predisposes to condition' (chemical or drug or treatment) too restrictive?

Issue - State: open - Opened by bill-baumgartner 5 months ago
Labels: question

#1510 - Add a description to AgentTypeEnum

Pull Request - State: closed - Opened by nicholsn 5 months ago

#1509 - TRAPI multi-CURIE query use cases semantics

Pull Request - State: open - Opened by RichardBruskiewich 6 months ago

#1509 - TRAPI multi-CURIE query use cases semantics

Pull Request - State: closed - Opened by RichardBruskiewich 6 months ago

#1508 - Bump requests from 2.31.0 to 2.32.0

Pull Request - State: closed - Opened by dependabot[bot] 6 months ago
Labels: dependencies

#1508 - Bump requests from 2.31.0 to 2.32.0

Pull Request - State: closed - Opened by dependabot[bot] 6 months ago
Labels: dependencies

#1507 - It seems impossible to instantiate GeneToGoTermAssociation objects using the python classes

Issue - State: open - Opened by KeithKelleher 6 months ago
Labels: bug

#1507 - It seems impossible to instantiate GeneToGoTermAssociation objects using the python classes

Issue - State: open - Opened by KeithKelleher 6 months ago
Labels: bug

#1506 - restore enumeration to use just for denormalized node properties for …

Pull Request - State: closed - Opened by sierra-moxon 6 months ago

#1505 - fix for Issue #1480

Pull Request - State: closed - Opened by sierra-moxon 6 months ago

#1504 - Fix biolink:treats (and related) mixin predicate(s) to connect with related_to hierarchy

Pull Request - State: closed - Opened by RichardBruskiewich 6 months ago

#1503 - What is the Prefix for microRNA?

Issue - State: open - Opened by codewarrior2000 6 months ago
Labels: question, identifiers

#1502 - Bump jinja2 from 3.1.3 to 3.1.4

Pull Request - State: closed - Opened by dependabot[bot] 6 months ago
Labels: dependencies

#1501 - Bump tqdm from 4.66.1 to 4.66.3

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago
Labels: dependencies

#1500 - make necessary changes to id_prefixes for chemical entity hierarchy

Pull Request - State: closed - Opened by sierra-moxon 7 months ago

#1499 - Sequence Motif PWMs

Issue - State: open - Opened by riyavsinha 7 months ago
Labels: question, LinkML

#1498 - Pathway `preceded_by`/`followed_by`

Issue - State: open - Opened by riyavsinha 7 months ago - 2 comments
Labels: question, working-group/predicates

#1497 - Add p_value & adjusted_p_value slots to Association class

Pull Request - State: closed - Opened by kevinschaper 7 months ago

#1496 - Generated Python/Pydantic Models as Package?

Issue - State: open - Opened by riyavsinha 7 months ago - 1 comment
Labels: question, LinkML

#1495 - Additional RO term to has_phenotype

Pull Request - State: closed - Opened by kevinschaper 7 months ago

#1494 - Prediction Qualifiers

Issue - State: open - Opened by riyavsinha 7 months ago - 2 comments
Labels: question

#1493 - Move prefix map to src

Issue - State: open - Opened by gaurav 7 months ago
Labels: identifiers, devops

#1492 - add 'url' property with a description that was difficult to write in …

Pull Request - State: closed - Opened by sierra-moxon 7 months ago - 7 comments

#1491 - update predicate mapping to refer to qualified predicates for regulates

Pull Request - State: closed - Opened by sierra-moxon 7 months ago - 3 comments

#1490 - revert semmed mappings for associated_with and administrated_to in root level yaml file

Pull Request - State: closed - Opened by sierra-moxon 7 months ago

#1490 - revert semmed mappings for associated_with and administrated_to in root level yaml file

Pull Request - State: closed - Opened by sierra-moxon 7 months ago

#1489 - 4.2.0

Pull Request - State: closed - Opened by sierra-moxon 7 months ago

#1488 - Bump idna from 3.6 to 3.7

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago
Labels: dependencies

#1487 - Add klat

Pull Request - State: closed - Opened by kevinschaper 7 months ago

#1486 - A URL from Reactome database

Issue - State: open - Opened by codewarrior2000 8 months ago - 11 comments
Labels: question, working-group/MolePro

#1486 - A URL from Reactome database

Issue - State: open - Opened by codewarrior2000 8 months ago - 1 comment
Labels: question, working-group/MolePro

#1485 - Two discrepencies in `OMIM` prefix

Issue - State: open - Opened by gaurav 8 months ago
Labels: identifiers

#1485 - Two discrepencies in `OMIM` prefix

Issue - State: open - Opened by gaurav 8 months ago
Labels: identifiers

#1484 - `biolink` base namespace does not redirect correctly?

Issue - State: open - Opened by matentzn 8 months ago - 1 comment
Labels: bug, identifiers

#1484 - `biolink` base namespace does not redirect correctly?

Issue - State: open - Opened by matentzn 8 months ago
Labels: bug, identifiers

#1483 - Make the hierarchy is-a complete

Issue - State: open - Opened by cmungall 8 months ago
Labels: enhancement, next release candidate

#1482 - Obsolete Bacterium, or place it correctly

Issue - State: open - Opened by cmungall 8 months ago

#1481 - Update biolink-model.yaml

Pull Request - State: closed - Opened by mbrush 8 months ago

#1480 - Inverses of mixin predicates don't establish an is_a path to a "root" mixin

Issue - State: open - Opened by sierra-moxon 8 months ago
Labels: working-group/predicates, next release candidate