Table 1

Example services using various SideCache features

Web Service / Type / Operation

Purpose/Example

Data Source


GeneInfoWS data web service getInfo

Inputs a list of NCBI gene IDs and returns name, chromosome number, and chromosome start position of the corresponding genes. http://visual.cs.utsa.edu/GeneInfoWS?operation=getInfo&sourceSpecies=9606&genes=7157,20,672 webcite

NCBI


GeneInfoWS data web service getIds

Inputs a list of gene names and returns a list of the corresponding NCBI gene IDs. http://visual.cs.utsa.edu/GeneInfoWS?operation=getIds&sourceSpecies=9606&genes=TP53,ABCA2,BRCA1 webcite

NCBI


GeneInfoWS data web service getInteractants

Inputs a list of NCBI gene IDs and returns a list of NCBI gene IDs for the genes whose products interact with the products of the input genes. The results for both input and output gene IDs include gene name, chromosome and chromosome start position. http://visual.cs.utsa.edu/GeneInfoWS?operation=getInteractants&sourceSpecies=9606&genes=7157,20,672 webcite

NCBI


GeneInfoWS data web service getVersions

Returns a list of provenance data including a version identifier as well as creation date, size and source for each file. http://visual.cs.utsa.edu/GeneInfoWS?operation=getVersions webcite


GeneInfoWS data web service versioned getInfo

Inputs a list of NCBI gene IDs and returns name, chromosome number, and chromosome start position of the corresponding genes. http://visual.cs.utsa.edu/GeneInfoWS?operation=getInfo&sourceSpecies=9606&genes=7157,20,672&versionIdentifier=1296771389679(getid) webcite

NCBI


EnrichWS data web service goEnrichment

Inputs a list of NCBI gene IDs, GO type, IEA evidence inclusion, a maximum group count and species. The service returns groups of gene IDs that are enriched for particular GO terms. The results include term, group members and group p-value. The number of groups is limited by the input group count. http://visual.cs.utsa.edu/EnrichWS?enrichType=goEnrichment&calc=Parent-Child-Union&species=9606&genes=1499|7827|2719|5002&max=10&evid=_IEA_&type=Component webcite

Gene ontology from NCBI


EnrichWS data web service meshEnrichment

Inputs a list of NCBI gene IDs, a maximum group count, and taxonomy ID. The service returns the enriched MeSH terms, their corresponding enriched members, and the p-value for that group. The number of groups is limited by the input group count. http://visual.cs.utsa.edu/EnrichWS?enrichType=meshEnrichment&calc=Parent-Child-Union&species=9606&genes=1499|7827|2719|5002&max=10 webcite

Gene2MeSH from NCIBI


EnrichWS data web service getVersions

Returns a list of provenance data including a version identifier as well as creation date, size and source for each file. http://visual.cs.utsa.edu/EnrichWS?enrichType=getVersions webcite


OrthologWS data web service default

Inputs a list of NCBI gene IDs, the source species taxonomy ID, and the target species taxonomy ID. The service returns all orthologs and the percent identity shared between the products of the source and target genes. http://visual.cs.utsa.edu/OrthologWS?sourceSpecies=9606&targetSpecies=10090&genes=7157,20,672 webcite

Ensembl


OrthologWS data web service getVersions

Returns a list of provenance data including a version identifier as well as creation date, size and source for each file. http://visual.cs.utsa.edu/OrthologWS?operation=getVersions webcite


ProxyWS proxy web service uml

Returns the results from the input UML. Manages caching for efficient retrievals, and timing of external web site calls. http://visual.cs.utsa.edu/ProxyWS/Proxy?url=http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id=7157,20,672&retmode=xml webcite


Doderer et al. BMC Research Notes 2011 4:182   doi:10.1186/1756-0500-4-182

Open Data