dipper

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I just noticed that at least one of the identifiers that we are currently reliant on in our cypher queries is now obsoleted in GENO. it is possible that other...

nlwashington

Update IRIs for 'qualifier' and 'quantifier' association properties

1

The has_qualifier and has_quantifier properties that hang from some associations were originally created with a GENO namespace, but have since been ceded to SEPIO where they are more in scope....

mbrush

Update Source: GO associations

7

* [ ] better document GeneOntology.py * e.g. IMP annotations generate an additional phenotype annotation * other annotations go in with one of 3 RO types * [ ] fix...

cmungall

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...

kshefchek

Modeling genetic/genomic mapping locations

2

We need to properly model genetic/genomic landmark locations. For example: (current ZFIN refactor) http://zfin.org/action/mapping/detail/ZDB-SSLP-980528-17 In ZFIN, we have mappings of different features (genes, sequence variants, ESTs, cDNA, SNPs, etc.) by...

bryanlaraway

We will be bringing in some test antibody data from ZFIN to pilot test a "resource" tab and related search functionality. This should be done with @bryanlaraway and @mbrush to...

mellybelly

We've recently encountered poorly formed IRIs that resulted from most-likely erroneous ids coming from data providers. For example: "/S0100-879X2005000100006" was coming as a DOI fragment, which we expand out to...

nlwashington

add pub fetcher as post-processing utility

1

in order to display the publications that any source contains with nice labels, it would be prudent to fetch the publication details from pubmed, if they are available. this could...

nlwashington

Morpholinos are appearing as variants in the app.

3

For example, the variant tab here (https://monarchinitiative.org/gene/ZFIN:ZDB-GENE-030131-3776) lists three morpholinos as variants. Tracked the problem to the cypher queries that do not exclude morpholinos from being loaded into solr. e.g....

mbrush

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...

kshefchek