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PATRIC3 / patric3_website

Legacy PATRIC Website (JBoss Portal Version)
MIT License
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data types for id mapper should be generated from what is currently available in solr #1882

Open JoshuaVSherman opened 6 years ago

mshukla1 commented 5 years ago

Given ID mapping table doesn't get updated that often and that it will be costly to get the list dynamically every time the page is loaded, I am fine with having it cached, as long as it reflects what is in the database.

mshukla1 commented 5 years ago

@dawenx,

Below is the complete list of available ID types from the database. Please update the form dropdown accordingly.

PATRIC ID Feature ID Alt Locus Tag P2 Feature ID RefSeq (Protein ID) RefSeq Locus tag Gene ID GI Allergome ArachnoServer BioCyc BioGrid BioMuta CCDS CGD CRC64 ChEMBL ChiTaRS CleanEx CollecTF ConoServer DIP DMDM DNASU DisProt DrugBank EMBL EMBL-CDS ESTHER EchoBASE EcoGene Ensembl EnsemblGenome EnsemblGenome_PRO EnsemblGenome_TRS Ensembl_PRO Ensembl_TRS EuPathDB FlyBase GeneCards GeneDB GeneID GeneReviews GeneTree GeneWiki Gene_Name Gene_ORFName Gene_OrderedLocusName Gene_Synonym GenomeRNAi GuidetoPHARMACOLOGY H-InvDB HGNC HOGENOM HOVERGEN HPA KEGG KO LegioList Leproma MEROPS MGI MIM MINT MaizeGDB NCBI_TaxID OMA Orphanet OrthoDB PATRIC PDB PeroxiBase PharmGKB PomBase PseudoCAP REBASE RGD Reactome RefSeq RefSeq_NT SGD STRING SwissLipids TAIR TCDB TreeFam TubercuList UCSC UniGene UniParc UniPathway UniProtKB-ID UniRef100 UniRef50 UniRef90 VectorBase WBParaSite World-2DPAGE WormBase WormBase_PRO WormBase_TRS Xenbase ZFIN dictyBase eggNOG euHCVdb mycoCLAP neXtProt

mshukla1 commented 5 years ago

@dawenx, please look at the ID Mapping tool at the uniprot. I like us to organize id types by groups to make them more useful. See the screenshot.

https://www.uniprot.org/uploadlists/

Screen Shot 2019-04-19 at 7 26 04 AM
dawenx commented 5 years ago

i checked out uniprot site, but it's not clear to me how to classify. if you could add a group name for each id type, then export a list similar to uniprot, i can update the UI to reflect your list. we can order group by importance, but i strongly suggest to order id types within a group alphabetically. @mshukla1

dawenx commented 5 years ago

i'm going through my active but stalled tickets... @mshukla1 do you have time to provide the information i requested last week?

mshukla1 commented 5 years ago

Attached is the list of group names and corresponding id types. Could not put it in the git hub comment as It does not keep the formatting.

Let me know if you have any questions.

-Maulik

On May 21, 2019, at 3:00 PM, Dawen Xie notifications@github.com<mailto:notifications@github.com> wrote:

i'm going through my active but stalled tickets... @mshukla1https://github.com/mshukla1 do you have time to provide the information i requested last week?

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