Data · dataset · 2020
Gold Stamp IDs to SRA IDs convertion of the metagenomes of GEMs
Listed in Researchdata.se and Swedish National Data Service — shown once because both records carry DOI 10.17044/scilifelab.13246817
Description
A small simple JSON-file containing the mapping from Gold Stamp IDs from the IMG/JGI database to the SRA IDs useable by fastq-dump to download the corresponding metagenomes from NCBI. The GoldIDs are the ones from the Supplemental Table 1 from Nayfach, S., Roux, S., Seshadri, R. et al. A genomic catalog of Earth’s microbiomes. Nat Biotechnol (2020). doi.org/10.1038/s41587-020-0718-6, that have been submited to the Short Read Archive.
The code used to generate this mapping is available at github.com/moritzbuck/jgi2sra_mapper
Links
Where it is published
- DOI doi.org/10.17044/scilifelab.13246817 ↗
DOI / persistent id · from researchdata se
Catalogue records · 2
- OAI-PMH record api.researchdata.se/oai-pmh?verb=GetRecord&metadataPrefix=oai_dc&identifier=oai%3A… ↗
metadata API · from researchdata se
- OAI-PMH record snd.se/oai-pmh?verb=GetRecord&metadataPrefix=oai_dc&identifier=oai%3A… ↗
metadata API · from snd se
Topics
- From keywords
- Earth & Environmental Science · Earth & Environmental Science · Ecology · Ecology · Life Sciences · Life Sciences · Medicine & Health · Medicine & Health
- Inferred from text
- Tabular 65%
Related
- Possibly the same asGold Stamp IDs to SRA IDs convertion of the metagenomes of GEMs
Provenance · 2 source records, 12 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| Researchdata.se | oai:researchdata.se:doi-10-17044-scilifelab-13246817/0 | 14 d ago | JSON v1 |
| Swedish National Data Service | oai:researchdata.se:doi-10-17044-scilifelab-13246817/0 | 3 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| concepts[field].anzsrc:group:3103 | mapping · researchdata se | vocabulary-mapper@1.0.0 | keywords['Ecology'] |
| concepts[field].anzsrc:group:3103 | mapping · snd se | vocabulary-mapper@1.0.0 | keywords['Ecology'] |
| concepts[field].local:field:earth-environmental | mapping · snd se | connector:snd_se@1.0.0 | |
| concepts[field].local:field:earth-environmental | mapping · researchdata se | connector:researchdata_se@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · snd se | connector:snd_se@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · researchdata se | connector:researchdata_se@1.0.0 | |
| concepts[field].local:field:medicine-health | mapping · researchdata se | connector:researchdata_se@1.0.0 | |
| concepts[field].local:field:medicine-health | mapping · snd se | connector:snd_se@1.0.0 | |
| concepts[modality].local:modality:tabular | enrichment · researchdata se | keyword-concept-rules@1.0.0 | title+description (65%) |
| description | source · researchdata se | connector:researchdata_se@1.0.0 | /metadata/dc/description |
| publication_date | source · researchdata se | connector:researchdata_se@1.0.0 | |
| title | source · researchdata se | connector:researchdata_se@1.0.0 | /metadata/dc/title |