metadata

INSDC Sequences

Dernière version Publié par Test Organization #1 le 24 juin 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=""`... plus
Date de publication:
24 juin 2021
Hébergé par:
Test Organization #1
Licence:
CC-BY 4.0

Description

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

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Versions

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Droits

Les chercheurs doivent respecter la déclaration de droits suivante:

L’éditeur et détenteur des droits de cette ressource est Test Organization #1. This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.

Enregistrement GBIF

Cette ressource a été enregistrée sur le portail GBIF, et possède l'UUID GBIF suivante : fe39cd36-6580-4205-bfe2-ca19990521fd.  Test Organization #1 publie cette ressource, et est enregistré dans le GBIF comme éditeur de données avec l'approbation du GBIF Secretariat.

Mots-clé

Metadata

Contacts

Personne ayant créé cette ressource:

European Bioinformatics Institute (EMBL-EBI)

Personne pouvant répondre aux questions sur la ressource:

European Bioinformatics Institute (EMBL-EBI)

Personne ayant renseigné les métadonnées:

GBIF Helpdesk

Autres personnes associées à la ressource:

Utilisateur
Marie Grosjean

Couverture géographique

Worldwide

Enveloppe géographique Sud Ouest [-90, -180], Nord Est [90, 180]

Métadonnées additionnelles

Identifiants alternatifs fe39cd36-6580-4205-bfe2-ca19990521fd
https://ipt.gbif.org/resource?r=marie-test-embl-metadata