metadata

INSDC Sequences

Última versión Publicado por Test Organization #1 en 24 de junio de 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=""`... Más
Fecha de publicación:
24 de junio de 2021
Alojado por:
Test Organization #1
Licencia:
CC-BY 4.0

Descripción

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

Descargas

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Versiones

La siguiente tabla muestra sólo las versiones publicadas del recurso que son de acceso público.

Derechos

Los usuarios deben respetar los siguientes derechos de uso:

El publicador y propietario de los derechos de este trabajo es Test Organization #1. This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.

Registro GBIF

Este recurso ha sido registrado en GBIF con el siguiente UUID: fe39cd36-6580-4205-bfe2-ca19990521fd.  Test Organization #1 publica este recurso, y está registrado en GBIF como un publicador de datos avalado por GBIF Secretariat.

Palabras clave

Metadata

Contactos

¿Quién creó el recurso?:

European Bioinformatics Institute (EMBL-EBI)

¿Quién puede resolver dudas acerca del recurso?:

European Bioinformatics Institute (EMBL-EBI)

¿Quién documentó los metadatos?:

GBIF Helpdesk

¿Quién más está asociado con el recurso?:

Usuario
Marie Grosjean

Cobertura geográfica

Worldwide

Coordenadas límite Latitud Mínima Longitud Mínima [-90, -180], Latitud Máxima Longitud Máxima [90, 180]

Metadatos adicionales

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