Kent Shefchek

We need support for drug combinations and their associations, in addition to binary chemical/drug -> phenotype/disease/gene associations. I'm not sure where this fits - perhaps we need a new Chemicals...

Review StringDB ingest now that they are cc-by

2

Thanks in part to @mellybelly @kltm @lwinfree and all the reusable data team, StringDB is now all cc-by, so we can pull a lot more data. Currently we are only...

MyChem ingest outputting empty file

1

I need to debug this, but at present the ingest outputs a file with minimal metadata triples. Looks like it it is failing on an initial call: DEBUG:urllib3.connectionpool:http://mychem.info:80 "POST /v1/drug?ids=RTAQQCXQSZGOHL-UHFFFAOYSA-N%2CWFKWXMTUELFFGS-UHFFFAOYSA-N%2CPXHVJJICTQNCMI-UHFFFAOYSA-N%2CSYQBFIAQOQZEGI-UHFFFAOYSA-N%2CGNPVGFCGXDBREM-UHFFFAOYSA-N%2CBUGBHKTXTAQXES-UHFFFAOYSA-N%2CQCWXUUIWCKQGHC-UHFFFAOYSA-N%2CWATWJIUSRGPENY-UHFFFAOYSA-N%2CLFNLGNPSGWYGGD-UHFFFAOYSA-N%2CTVFDJXOCXUVLDH-UHFFFAOYSA-N&fields=drugbank.targets%2Cdrugbank.drugbank_id%2Cunii.unii%2Cdrugcentral.drug_use%2Cdrugcentral.bioactivity...

Question: how to ingest and model "phenotype manifest in" data from FlyBase

3

How do we handle "phenotype manifest in" data? - Link them to the anatomical entity via 'located in' or 'expressed in' and/or; - Link them to UPheno classes with 'has...

Refactor landing pages to pull data from SciGraph and/or Golr

1

Currently the landing page "spotlight" area pulls data from NIF views. We want to refactor this to pull data from SciGraph dynamic services and/or the Golr views.

Incorrect MONDO ids as HPO annotation source

1

(This is not an app issue but unsure where to put this ticket) The HPO annotation ingest currently links OMIM as a source for associations, which is accurate. However, in...

Disambiguate counts on data tabs/tables

8

Any given data table has three types of counts 1. Distinct associations between X (and subclasses) and Y 2. Distinct Y 3. Distinct classes in closure For example, on a...

GBA incorrectly associated with Niemann-Pick disease type B

4

From https://www.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM16193&product=CC > donor subject is also heterozygous for an A>G transition at nucleotide 1226 in exon 9 of the GBA gene (1226A>G) resulting in a substitution of serine for...

Right now our barcharts embed html forms in the svg element using the foreignObject element. However this is a relatively new feature and there are many [bugs associated with its...

Now that we have a [cypher service in scigraph](https://scigraph-data-dev.monarchinitiative.org/scigraph/docs/#!/cypher/execute), we should add a service in monarch that proxies this, and make a small UI with monarch specific examples (gene-phenotype, ortholog-phenotype)....