NaturalHistoryMuseum / scratchpads2

Scratchpads 2.0
http://scratchpads.org
GNU General Public License v2.0
199 stars 83 forks source link

Docs: update to explain when NCBI expected to show data in Scratchpads #6604

Open therobyouknow opened 2 years ago

therobyouknow commented 2 years ago

https://github.com/NaturalHistoryMuseum/scratchpads2/issues/6594#issuecomment-1316879613

I will ooen a new ticket for documentation specifically to provide more info on how ncbi works with taxonomy terms.

Example screenshots in that other comment could be used for this documentation update

Archilegt commented 2 years ago

See Smith et al. (2009: 11, table 1):

Module Name: ncbi Description: Searches the NCBI database for nucleotide sequences, protein sequences and related links. NCBI database API: http://www.programmableweb.com/api/ncbi-entrez

See also Smith et al. (2011: 61):

Taxon pages Scratchpad taxon pages provide a mechanism for users to dynamically construct and curate pages of information about any taxon selected from the site’s biological taxonomy. These pages use taxonomic names as a search term to integrate tagged content in a Scratchpad with third party content external to the site. This third party content draws upon a variety of external data sources (e.g. Biodiversity Heritage Library, flickr, GBIF and NCBI Genbank), which have suitable APIs that support this type of integration.

Archilegt commented 2 years ago

For referring the manual users to the NCBI Taxonomy database: Schoch CL, et al. NCBI Taxonomy: a comprehensive update on curation, resources and tools. Database (Oxford). 2020: baaa062. https://doi.org/10.1093/database/baaa062

For referring the manual users to the NCBI GenBank: Sayers EW, et al. GenBank. Nucleic Acids Res. 2019. 47(D1):D94-D99. https://doi.org/10.1038/s41586-022-05292-x