metadata

INSDC Sequences

最新バージョン Test Organization #1 によって公開 2021/06/24 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=""`... 以上
公開日:
2021/06/24
ホスト::
Test Organization #1
ライセンス:
CC-BY 4.0

説明

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

ダウンロード

メタデータのみリソース のメタデータの最新版をEML または RTF としてダウンロード:

EML ファイルとしてのメタデータ ダウンロード English で (6 kB)
RTF ファイルとしてのメタデータ ダウンロード English で (6 kB)

バージョン

次の表は、公にアクセス可能な公開バージョンのリソースのみ表示しています。

権利

研究者は権利に関する下記ステートメントを尊重する必要があります。:

パブリッシャーとライセンス保持者権利者は Test Organization #1。 This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.

GBIF登録

このリソースをはGBIF と登録されており GBIF UUID: fe39cd36-6580-4205-bfe2-ca19990521fdが割り当てられています。   GBIF Secretariat によって承認されたデータ パブリッシャーとして GBIF に登録されているTest Organization #1 が、このリソースをパブリッシュしました。

キーワード

Metadata

連絡先

リソースを作成した人:

European Bioinformatics Institute (EMBL-EBI)

リソースに関する質問に答えることができる人:

European Bioinformatics Institute (EMBL-EBI)

メタデータを記載した人:

GBIF Helpdesk

他に、リソースに関連付けられていた人:

データ利用者
Marie Grosjean

地理的範囲

Worldwide

座標(緯度経度) 南 西 [-90, -180], 北 東 [90, 180]

追加のメタデータ

代替識別子 fe39cd36-6580-4205-bfe2-ca19990521fd
https://ipt.gbif.org/resource?r=marie-test-embl-metadata