qualifiers / biolink3 update #106
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…and added qualifiers section
allosteric_modulator, antagonist, blocker, inhibitor, inverse_agonist, modulator, partial_agonist, positive_modulator (and commented-out ones like inducer, inhibitory_allosteric_modulator, negative_modulator, suppressor) and their reverse operations
…caused_by not in biolink model 3.0.2, but might be in a later release
for decreases_expression_of
…_process, process_negatively_regulates_process predicates
…r qualifier-refactor
…r qualifier-refactor
…for biolink 3.0.2
…nition of associated_with in biolink 3.0.2
most update to biolink:source_web_page
…ink terms for some), comments
edit some api descriptions, add comments, remove temporary yamls for bte/service provider
use other branch to get qualifier-refactor for this api https://github.com/NCATS-Tangerine/translator-api-registry/blob/biolink3-textMining/text_mining/smartapi.yaml
due to ambiguity of semmeddb relationship vs biolink-model definition of regulates https://github.com/biolink/biolink-model/blob/v3.0.3/biolink-model.yaml\#L3797
mapping semmeddb associated_with to biolink related_to mapping semmeddb augments and stimulates to biolink affects (obj_aspect: activity_or_abundance, obj_direction: increased) mapping semmeddb inhibits to biolink affects (obj_aspect: activity_or_abundance, obj_direction: decreased) and having correct reverse operations for augments, stimulates, and inhibits
due to removing the abstract label from biolink interacts_with predicate biolink/biolink-model#1171
… test-data url to default
no difference in output
|
Related to biothings/biothings_explorer#512 and biothings/biothings_explorer#514 |
add biothings and/or make second word of api names capitalized
annotation covers less chemical records in chem -> gene direction (forward/indexed), but uses more specific predicate-qualifier modeling annotation still covers all chemical records in gene -> chem direction (reverse), but predicate has been changed to more-general interacts_with
…support will work with biothings/api-respone-transform.js#44 to add node labels when SRI Node Normalizer doesn't related to biothings/biothings_explorer#539 but for instances that don't have the PR's code, the response-mappings will become normal edge-attributes
not using list_filter for more specific predicate modeling in chem->gene direction for an example of more-specific work, see 5d4391a
…and mod operation
…t automatically use gene-ortholog intermediate
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Don't merge until we're ready to move to qualifiers / biolink3 for all BTE instances.