This dataset contains INSDC sequence records not associated with environmental sample identifiers or host organisms. The dataset is prepared periodically using the public ENA API (https://www.ebi.ac.uk/ena/portal/api/) by querying data with search parameters: `environmental_sample=False & host=""`
EMBL-EBI also publishes other records in separate datasets (https://www.gbif.org/publisher/ada9d123-ddb4-467d-8891-806ea8d94230).
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 taxonomy checklist available here: http://ftp.ebi.ac.uk/pub/databases/ena/taxonomy/sdwca.zip
More information available here: https://github.com/gbif/embl-adapter#readme
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
GBIF url: https://www.gbif.org/dataset/d8cd16ba-bb74-4420-821e-083f2bac17c2
Citation: European Bioinformatics Institute (EMBL-EBI), GBIF Helpdesk (2024). INSDC Sequences. Version 1.82. European Nucleotide Archive (EMBL-EBI). Occurrence dataset https://doi.org/10.15468/sbmztx accessed via GBIF.org on 2024-04-29.
物種 | 原始紀錄物種 | 類群 | 日期 | 行政區 | 資料集 | |
---|---|---|---|---|---|---|
Cephalotaxus 粗榧屬 | Cephalotaxus harringtonia var. wilsoniana | 裸子植物 | 2020-04-01 | INSDC Sequences | ||
Dengue virus | 2001-01-01 | INSDC Sequences | ||||
Sargassum ilicifolium Turner C.Agardh 1820 冬青葉馬尾藻 | Sargassum ilicifolium | 原藻類 | 2017-02-13 | INSDC Sequences | ||
Hymenopellis | Hymenopellis furfuracea | 真菌類 | 2019-01-01 | INSDC Sequences | ||
Meretrix 文蛤屬 | Meretrix sp. n. STH-2020 | 蝸牛與貝類 | 2018-07-31 | INSDC Sequences | ||
Bufo bankorensis 盤古蟾蜍 | Bufo bankorensis | 兩棲類 | 2019-05-05 | INSDC Sequences | ||
Simulium 蚋屬 | Simulium jianshiense | 其他昆蟲 | INSDC Sequences | |||
Lomariopsis 羅蔓藤蕨屬 | Lomariopsis boninensis | 蕨類 | 2020-09-10 | INSDC Sequences | ||
Halymenia durvillei | 2009-05-23 | INSDC Sequences | ||||
Taiwanofungus camphoratus 樟芝 | Taiwanofungus camphoratus | 真菌類 | 2003-08-01 | INSDC Sequences | ||
Geothelphusa olea 黃綠澤蟹 | Geothelphusa olea | 蝦蟹類 | 2001-10-25 | INSDC Sequences | ||
Venturia 黑星菌屬 | Venturia nashicola | 真菌類 | 2007-04-27 | INSDC Sequences | ||
Lactiplantibacillus plantarum | INSDC Sequences | |||||
Pseudomonas sp. NTUIOB KSE8 | 2011-05-11 | INSDC Sequences | ||||
Planaeschna risi; Planaeschna risi risi 李斯晏蜓; 李斯晏蜓(risi亞種) | Planaeschna risi | 蜻蛉類 | 2007-10-20 | INSDC Sequences | ||
Weissella confusa | 2012-12-06 | INSDC Sequences | ||||
Centrosema pubescens Benth. 山珠豆 | Centrosema pubescens | 被子植物 | INSDC Sequences | |||
dengue virus type 3 | 1998-01-01 | INSDC Sequences | ||||
Chilli veinal mottle virus | 1996-01-01 | INSDC Sequences | ||||
Hylarana latouchii 拉都希氏赤蛙 | Hylarana latouchii | 兩棲類 | INSDC Sequences | |||
Ophion bicarinatus 雙脊瘦姬蜂 | Ophion bicarinatus | 其他昆蟲 | INSDC Sequences | |||
Dryopteris hasseltii (Blume) C.Chr. 哈氏鱗毛蕨 | Dryopteris hasseltii | 蕨類 | INSDC Sequences | |||
Coxsackievirus A4 | 2006-01-01 | INSDC Sequences | ||||
Epinephelus fuscoguttatus 棕點石斑魚 | Epinephelus fuscoguttatus | 魚類 | INSDC Sequences | |||
Saccostrea scyphophilla 黑齒牡蠣 | Saccostrea mordax | 蝸牛與貝類 | 2009-06-11 | INSDC Sequences |