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RTXteam / RTX

Software repo for Team Expander Agent (Oregon State U., Institute for Systems Biology, and Penn State U.)
https://arax.ncats.io/
MIT License
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Add ranker handling for infores:tcga biolink:has_evidence attribute #1786

Open finnagin opened 2 years ago

finnagin commented 2 years ago

Some examples here: https://arax.ncats.io/beta/?r=36527

example edge attribute list containing the attribute of interest:

--
attribute_type_id: | biolink:aggregator_knowledge_source
value_type_id: | biolink:InformationResource
value: | infores:biothings-explorer
 ---
attribute_type_id: | Contribution
value_type_id: | biolink:has_evidence
value: | -0.25074358634572425
 ---
attribute_source: | infores:connections-hypothesis
attribute_type_id: | biolink:primary_knowledge_source
description: | The Connections Hypothesis Provider from NCATS Translator.
value_type_id: | biolink:InformationResource
value_url: | http://chp.thayer.dartmouth.edu
value: | infores:connections-hypothesis
 ---
attribute_source: | infores:gdc
attribute_type_id: | biolink:supporting_data_source
description: | The Cancer Genome Atlas provided by the GDC Data Portal.
value_type_id: | biolink:InformationResource
value_url: | https://portal.gdc.cancer.gov/
value: | infores:tcga
 ---
attribute_source: | infores:connections-hypothesis
attribute_type_id: | biolink:supporting_data_source
description: | Documents how Connections Hypothesis Provider builds ranked contribution values over tcga data.
value_type_id: | biolink:InformationResource
value_url: | https://di2ag.github.io/chp/chp_documentation#chp-single-hop-contribution-analysis
value: | infores:tcga
 ---
attribute_source: | infores:arax
attribute_type_id: | biolink:knowledge_source
description: | ARAX  inserted this attribute because the KP (BTE) did not seem to provide  such an attribute (indicating that this edge came from them).
value_type_id: | biolink:InformationResource
value: | infores:biothings-explorer
 ---
attribute_source: | infores:arax
attribute_type_id: | biolink:aggregator_knowledge_source
value_type_id: | biolink:InformationResource
value: | infores:arax
---
attribute_type_id:  biolink:aggregator_knowledge_source
value_type_id:  biolink:InformationResource
value:  infores:biothings-explorer
attribute_type_id:  Contribution
value_type_id:  biolink:has_evidence
value:  -0.25074358634572425
---
attribute_source:   infores:connections-hypothesis
attribute_type_id:  biolink:primary_knowledge_source
description:    The Connections Hypothesis Provider from NCATS Translator.
value_type_id:  biolink:InformationResource
value_url:  http://chp.thayer.dartmouth.edu/
value:  infores:connections-hypothesis
---
attribute_source:   infores:gdc
attribute_type_id:  biolink:supporting_data_source
description:    The Cancer Genome Atlas provided by the GDC Data Portal.
value_type_id:  biolink:InformationResource
value_url:  https://portal.gdc.cancer.gov/
value:  infores:tcga
---
attribute_source:   infores:connections-hypothesis
attribute_type_id:  biolink:supporting_data_source
description:    Documents how Connections Hypothesis Provider builds ranked contribution values over tcga data.
value_type_id:  biolink:InformationResource
value_url:  https://di2ag.github.io/chp/chp_documentation#chp-single-hop-contribution-analysis
value:  infores:tcga
---
attribute_source:   infores:arax
attribute_type_id:  biolink:knowledge_source
description:    ARAX inserted this attribute because the KP (BTE) did not seem to provide such an attribute (indicating that this edge came from them).
value_type_id:  biolink:InformationResource
value:  infores:biothings-explorer
---
attribute_source:   infores:arax
attribute_type_id:  biolink:aggregator_knowledge_source
value_type_id:  biolink:InformationResource
value:  infores:arax
---
dkoslicki commented 2 years ago

Still TODO. Connections hypothesis provider are familiar with these, so liaise with them about what the ranges are etc.