metadata

INSDC Sequences

Последняя версия опубликована Test Organization #1 24 июня 2021 г. 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=""`... Больше
Дата публикации:
24 июня 2021 г.
Техническое обеспечение:
Test Organization #1
Лицензия:
CC-BY 4.0

Описание

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

Загрузки

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Версии

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Права

Исследователи должны соблюдать следующие права:

Публикующей организацией и владельцем прав на данную работу является Test Organization #1. This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.

Регистрация в GBIF

Этот ресурс был зарегистрирован в GBIF, ему был присвоен следующий UUID: fe39cd36-6580-4205-bfe2-ca19990521fd.  Test Organization #1 отвечает за публикацию этого ресурса, и зарегистрирован в GBIF как издатель данных при оподдержке GBIF Secretariat.

Ключевые слова

Metadata

Контакты

Кто является создателем ресурса:

European Bioinformatics Institute (EMBL-EBI)

Кто может ответить на вопросы о ресурсе:

European Bioinformatics Institute (EMBL-EBI)

Кем заполнены метаданные:

GBIF Helpdesk

Кто еще связан с данным ресурсом:

User
Marie Grosjean

Географический охват

Worldwide

Ограничивающие координаты Юг Запад [-90, -180], Север Восток [90, 180]

Дополнительные метаданные

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