mygene.info

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accept versioned Ensembl queries

1

http://mygene.info/v3/gene/ENSG00000123374.10 and http://mygene.info/v3/query?q=ENSG00000123374.10 return no hits, while http://mygene.info/v3/gene/ENSG00000123374 and http://mygene.info/v3/query?q=ENSG00000123374 return the expected result. Most people will not be searching versioned accession numbers (I don't think), but if this is...

andrewsu

CellMarker: a manually curated resource of cell markers in human and mouse Publication: https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gky900/5115823 Download page: http://biocc.hrbmu.edu.cn/CellMarker/download.jsp Head of human file: ``` speciesType tissueType2 cancerType cellType cellName3 cellMarker geneSymbol geneID...

andrewsu

drug-gene interaction database downloads page: http://www.dgidb.org/downloads see also https://github.com/biothings/mychem.info/issues/38

andrewsu

Using bt.hub.datatransform module, need to define a new "dict" edge which will lookup data from a dictionary instead of a mongo collection

sirloon

get genomic_pos data from NCBI?

2

Currently, our genomic_pos and genomic_pos_hg19 fields are coming from Ensembl, therefore, only available for those species included in Ensembl release. We should find out a good data source from NCBI...

newgene

Is this something of interest to restructure the homolog field in MyGene.info? Current structure: ``` "homologene": { "genes": [ [ 9606, 1017 ], [ 10090, 12566 ], [ 10116, 362817...

kevinxin90

Allow for exact matches only?

6

Querying something like "BRCA1", I get a lot of seemingly unrelated matches such as "BRAT1". This is obviously a symptom of the nature of ElasticSearch. In analytical use cases, personally,...

buchanae

Proteins with no genes

2

I think it would be useful for mygene to also store information about proteins with no associated Entrez record. For example: http://www.uniprot.org/uniprot/A2NXD2 http://www.uniprot.org/uniprot/Q5NV61

stuppie

I was expecting to find a link to the [mygene bioconductor package]( https://www.bioconductor.org/packages/release/bioc/html/mygene.html) from somewhere in [mygene.info documentation](http://docs.mygene.info/en/v3/index.html), but wasn't able to find it. (also, I don't think the official...

andrewsu

tuning of default search scoring for wildcard searches

3

I believe we have scoring in place to prioritize human, mouse, and rat over other species, and that seems to be working well: https://mygene.info/v3/query?q=BRCA2 But scoring with wildcard searches is...

andrewsu