INSDC Sequences

元數據EML檔	下載在 English 中 (6 KB)
元數據RTF文字檔	下載在 English 中 (6 KB)

說明

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

版本

以下的表格只顯示可公開存取資源的已發布版本。

權利

研究者應尊重以下權利聲明。:

此資料的發布者及權利單位為 Test Organization #1。 This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.

GBIF 註冊

此資源已向GBIF註冊，並指定以下之GBIF UUID: fe39cd36-6580-4205-bfe2-ca19990521fd。 Test Organization #1 發佈此資源，並經由GBIF Secretariat同意向GBIF註冊成為資料發佈者。

關鍵字

Metadata

聯絡資訊

European Bioinformatics Institute (EMBL-EBI)

出處 ●
連絡人

datasubs@ebi.ac.uk

http://www.ebi.ac.uk

GBIF Helpdesk

元數據提供者

helpdesk@gbif.org

Marie Grosjean

使用者

mgrosjean@gbif.org

地理涵蓋範圍

Worldwide

界定座標範圍	緯度南界經度西界 [-90, -180], 緯度北界經度東界 [90, 180]

額外的詮釋資料

替代的識別碼	fe39cd36-6580-4205-bfe2-ca19990521fd
	https://ipt.gbif.org/resource?r=marie-test-embl-metadata