Suzanna Lewis

Provide visual clue when a transcript is missing either the 5' or 3' end

2

Perhaps a squiggle? Or an ellipsis... (for example)

RNA seq reads need indication of orientation

9

Reads should be visually segregated (plus strand above, minus strand below) so that it is easier to see which gene models they support.

Returning non-JSON for a request

3

This URL returns "Failed to find class with ID: WB:WBGene00020993", which the JSON parser then barfs on: https://scigraph-data-dev.monarchinitiative.org/scigraph/graph/neighbors/WB:WBGene00020993.json?blankNodes=False&relationshipType=RO%3A0002205&entail=True&direction=OUTGOING&depth=1 The correct URL (below) returns JSON just fine. But whatever the insult...

enhancement to filter by the produced_by information issue #545

2

Includes test as well. Motivated by need to only obtain orthologs called by PANTHER

Inconsistent usage of attributes 'references' (GOLR) versus 'publications' (Monarch)

1

Looks like the two systems refer to the same thing using a different terminology. Happy with either, but would be good to have them consistent.

Slimmer should support either a list of IDs, or the tag that indicates the set of IDs (e.g. goslim_agr)

3

Would rather not need to hard code the list of IDs (will do for the nonce), but have this embedded in the ontology itself.

Need functions for determining term-to-term relatedness

10

Annotations vary considerably in precision, but for conciseness and to determine coverage, we need to be able to answer basic graph traversal questions. For example, given two terms is one...

Discrepancies in results for HP and GO (same slim query)

1

For GO/GOlr the results contain this: reference: [ "MGI:MGI:5299957", "PMID:22031545" ] For HP/Monarch the results contain this: publications: [ { id: "PMID:103464" }, { id: "PMID:19563798" }, { id: "PMID:4972360"...

These are needed for GA4GH meta-data. I pointed them here to GENO as an alternative to creating enums. If there is a better home that's fine, but let's try and...

odd identifier to protein showing up for NCBI gene

7

For example: human NCBI:5435. Searching for the encoding gene via the ENCODES relation returns several ENSEMBL proteins, UniProtKB:P61218, itself, and (oddly) "**:.well-known/genid/NCBIGene5435product**" Clearly not a legit ID