Data · dataset · 2020
Gold Stamp IDs to SRA IDs convertion of the metagenomes of GEMs
Listed in SciLifeLab Data Repository
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. <div>The GoldIDs are the ones from the Supplemental Table 1 from <i>Nayfach, S., Roux, S., Seshadri, R. et al. A genomic catalog of Earth’s microbiomes. Nat Biotechnol (2020). <a href="doi.org/10.1038/s41587-020-0718-6" rel="nofollow">doi.org/10.1038/s41587-020-0718-6</a></i>, that have been submited to the Short Read Archive. </div><div>The code used to generate this mapping is available at github.com/moritzbuck/jgi2sra_mapper</div><p></p>
Links
Where it is published
- DOI doi.org/10.17044/scilifelab.13246817.v1 ↗
DOI / persistent id · from figshare scilifelab se
Catalogue records · 1
- OAI-PMH record api.figshare.com/v2/oai?verb=GetRecord&metadataPrefix=oai_dc&identifier=oai%3Af… ↗
metadata API · from figshare scilifelab se
Topics
- From keywords
- Earth & Environmental Science · Life Sciences · Microbial ecology
- Inferred from text
- Tabular 65%
Related
- Possibly the same asGold Stamp IDs to SRA IDs convertion of the metagenomes of GEMs
Provenance · 1 source records, 9 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| SciLifeLab Data Repository | oai:figshare.com:article/13246817 | 5 h ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · figshare scilifelab se | connector:figshare_scilifelab_se@1.0.0 | |
| concepts[field].anzsrc:field:310703 | mapping · figshare scilifelab se | vocabulary-mapper@1.0.0 | keywords['Microbial ecology'] |
| concepts[field].local:field:earth-environmental | mapping · figshare scilifelab se | connector:figshare_scilifelab_se@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · figshare scilifelab se | connector:figshare_scilifelab_se@1.0.0 | |
| concepts[modality].local:modality:tabular | enrichment · figshare scilifelab se | keyword-concept-rules@1.0.0 | title+description (65%) |
| description | source · figshare scilifelab se | connector:figshare_scilifelab_se@1.0.0 | /metadata/dc/description |
| license | source · figshare scilifelab se | connector:figshare_scilifelab_se@1.0.0 | /metadata/dc/rights |
| publication_date | source · figshare scilifelab se | connector:figshare_scilifelab_se@1.0.0 | |
| title | source · figshare scilifelab se | connector:figshare_scilifelab_se@1.0.0 | /metadata/dc/title |