INSDC Sequences
Latest version published by Test Organization #1 on 24 June 2021 Test Organization #1

This dataset contains a subset of INSDC sequences available from the the public ENA API (https://www.ebi.ac.uk/ena/portal/api/). The dataset is prepared periodically. This dataset doesn't contain any record associated with environmental sample identifiers or records associated with any host organism. Records with environmental sample identifiers and host organism can be found in separate datasets published by EMBL-EBI. This translates into the following parameters when querying data with the ENA portal API search: `environmental_sample=False & host=""`

The data was then processed as follows: 1. Human sequences were excluded. 2. For non-CONTIG records, the sample accession number (when available) along with the scientific name were used to identify sequence records corresponding to the same individuals (or group of organism of the same species in the same sample). Only one record was kept for each scientific name/sample accession number. 3. Contigs and whole genome shotgun (WGS) records were added individually. 4. The records that were missing some information were excluded. Only records associated with a specimen voucher or records containing both a location AND a date were kept. 5. The records associated with the same vouchers are aggregated together. 6. A lot of records left corresponded to individual sequences or reads corresponding to the same organisms. In practise, these were "duplicate" occurrence records that weren't filtered out in STEP 2 because the sample accession sample was missing. To identify those potential duplicates, we grouped all the remaining records by `scientific_name`, `collection_date`, `location`, `country`, `identified_by`, `collected_by` and `sample_accession` (when available). Then we excluded the groups that contained more than 50 records. The rationale behind the choice of threshold is explained here: https://github.com/gbif/embl-adapter/issues/10#issuecomment-855757978 7. To improve the matching of the EBI scientific name to the GBIF backbone taxonomy, we incorporated the ENA taxonomic information. The kingdom, Phylum, Class, Order, Family, and genus were obtained from the ENA Browser API: https://www.ebi.ac.uk/ena/browser/api/

You can find the mapping used to format the EMBL data to Darwin Core Archive here: https://github.com/gbif/embl-adapter/blob/master/DATAMAPPING.md

GBIF EML RTF Versions Rights
Downloads

Download the latest version of the metadata-only resource metadata as EML or RTF:

Metadata as an EML file download in English (6 kB)
Metadata as an RTF file download in English (6 kB)
Versions

The table below shows only published versions of the resource that are publicly accessible.

Rights

Researchers should respect the following rights statement:

The publisher and rights holder of this work is Test Organization #1. This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.

GBIF Registration

This resource has been registered with GBIF, and assigned the following GBIF UUID: fe39cd36-6580-4205-bfe2-ca19990521fd.  Test Organization #1 publishes this resource, and is itself registered in GBIF as a data publisher endorsed by GBIF Secretariat.

Keywords

Metadata

Contacts

Who created the resource:

European Bioinformatics Institute (EMBL-EBI)

Who can answer questions about the resource:

European Bioinformatics Institute (EMBL-EBI)

Who filled in the metadata:

GBIF Helpdesk

Who else was associated with the resource:

User
Marie Grosjean
Geographic Coverage

Worldwide

Bounding Coordinates South West [-90, -180], North East [90, 180]
Additional Metadata
Alternative Identifiers fe39cd36-6580-4205-bfe2-ca19990521fd
https://ipt.gbif.org/resource?r=marie-test-embl-metadata