Cellbase gene services wrong behavior for for some genes (we've counted 3604 in GRCh37)

[jlfrueda]

Many of the gene-related services of cellbase return no information for certain genes for which entries actually exist in the database, most of them appearing in related queries such as transcript search, for example. The problem can be replicated using both HGNC names and Ensembl Ids.

We encountered these problem for 3406 genes in GRCh37 (which we mainly use).

For example, for RBP3, which appears in OMIM and so is important for diagnostics,

• https://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000265203;r=10:47348363-47357881;t=ENST00000584701
• http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000265203;r=HG1211_PATCH:47843819-47853323;t=ENST00000584701

we found that cellbase gets no results:

• http://bioinfo.hpc.cam.ac.uk/cellbase/webservices/rest/v4/hsapiens/feature/gene/RBP3/info
• http://bioinfo.hpc.cam.ac.uk/cellbase/webservices/rest/v4/hsapiens/feature/gene/ENSG00000107618/info
• http://bioinfo.hpc.cam.ac.uk/cellbase/webservices/rest/v4/hsapiens/feature/gene/ENSG00000265203/info

If we specify the assembly, results are found for GRCh38:

• http://bioinfo.hpc.cam.ac.uk/cellbase/webservices/rest/v4/hsapiens/feature/gene/RBP3/info?assembly=grch38

which returns E2F1 in addition to RBP3, but nothing for GRCh37:

• http://bioinfo.hpc.cam.ac.uk/cellbase/webservices/rest/v4/hsapiens/feature/gene/RBP3/info?assembly=grch37

Using its ensembl ID does not work either:

• http://bioinfo.hpc.cam.ac.uk/cellbase/webservices/rest/v4/hsapiens/feature/gene/ENSG00000107618/info?assembly=grch37

The gene is actually in the GRCh37 database, and can be found with

• http://bioinfo.hpc.cam.ac.uk/cellbase/webservices/rest/v4/hsapiens/feature/gene/search?name=RBP3&assembly=grch37

• http://bioinfo.hpc.cam.ac.uk/cellbase/webservices/rest/v4/hsapiens/feature/gene/search?id=ENSG00000107618&assembly=grch37

If one search for RBP3 and does not specify the assembly,

• http://bioinfo.hpc.cam.ac.uk/cellbase/webservices/rest/v4/hsapiens/feature/gene/search?name=RBP3

cellbase returns only the GRCh37 result, and not the GRCh38 one. This behavior is also seem with the ensembl Ids. While, as we saw,

• http://bioinfo.hpc.cam.ac.uk/cellbase/webservices/rest/v4/hsapiens/feature/gene/ENSG00000107618/info

finds no results,

• http://bioinfo.hpc.cam.ac.uk/cellbase/webservices/rest/v4/hsapiens/feature/gene/search?id=ENSG00000107618

finds the GRCh37 gene, but

• http://bioinfo.hpc.cam.ac.uk/cellbase/webservices/rest/v4/hsapiens/feature/gene/search?id=ENSG00000265203

finds no results. Both

• http://bioinfo.hpc.cam.ac.uk/cellbase/webservices/rest/v4/hsapiens/feature/gene/search?id=ENSG00000107618&assembly=grch37

• http://bioinfo.hpc.cam.ac.uk/cellbase/webservices/rest/v4/hsapiens/feature/gene/search?id=ENSG00000265203&assembly=grch38

seem to work fine. So, to sum up:

• feature/gene/RBP3/info: no results
• feature/gene/RBP3/info?assembly=grch37: no results
• feature/gene/RBP3/info?assembly=grch38: two results, RBP3 and E2F1
• feature/gene/ENSG00000107618/info: no results
• feature/gene/ENSG00000265203/info: no results
• feature/gene/ENSG00000107618/info?assembly=grch37: no results
• feature/gene/ENSG00000265203/info?assembly=grch38: success (??)
• feature/gene/search?name=RBP3: only GRCh37 result, but not GRCh38
• feature/gene/search?name=RBP3&assembly=grch37: success
• feature/gene/search?name=RBP3&assembly=grch38: success
• feature/gene/search?id=ENSG00000107618: success
• feature/gene/search?id=ENSG00000265203: no results
• feature/gene/search?id=ENSG00000107618&assembly=grch37: success
• feature/gene/search?id=ENSG00000265203&assembly=grch38: success

One can make several assumptions about gene/*/info and gene/search behaving inconsistently with respect to unspecified assemblies, but even so gene/RBP3/info?assembly=grch37, gene/ENSG00000107618/info?assembly=grch37, feature/gene/RBP3/info?assembly=grch38 or feature/gene/search?id=ENSG00000265203 should be returning the right results.