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ArctosDB / arctos

Arctos is a museum collections management system
https://arctos.database.museum
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Linking to whole genome identifiers #3068

Closed ccicero closed 2 years ago

ccicero commented 4 years ago

@Jegelewicz @campmlc @dustymc

I am trying to link MVZ:Bird:191951 to its genome sequence.

The full specifications and sequence are available at https://vgp.github.io/genomeark/Chiroxiphia_lanceolata/ Can/should we add GenomeArk as an other identifier? If not, how else to do this?

Also, there are links to primary and alternate assemblies in GenBank. https://www.ncbi.nlm.nih.gov/assembly/GCA_009829145.1 https://www.ncbi.nlm.nih.gov/assembly/GCA_009829205.1

I entered the URLs in Arctos in the prefix/string field for other IDs, but they are not resolving to the correct pages. What am I doing wrong? https://arctos.database.museum/guid/MVZ:Bird:191951

ccicero commented 3 years ago

Back to this issue: I just received an email notifying me of a paper that was published, using MVZ, UAM, and MSB samples among others. I created the pub in Arctos and linked it to a project I had created previously.

Here is part of the email: "For your records, the sequence data have since been deposited in GenBank under the accession number PRJNA678344. Each individual does not have it's own number, but rather pooled samples were submitted to GenBank (for reproducibility reasons)."

NCBI Accession/Project Biosamples with pooled specimens

The NCBI_Biosample is listed for each specimen in the source data (file attached here). Stager_Junco_sourcedata.xlsx

@campmlc @KyndallH @dustymc @Jegelewicz - From previous discussion, I plan to link from the Arctos record to the Biosample that's listed in the source data, e.g., https://www.ncbi.nlm.nih.gov/biosample/16793657 (identifier type same as https://arctos.database.museum/guid/MVZ:Bird:191951). Does that sound right to you?

dustymc commented 2 years ago

Tentatively merging with https://github.com/ArctosDB/arctos/issues/3652 - same thing??