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 | |
---|---|---|---|---|---|---|
Bletilla formosana (Hayata) Schltr. 臺灣白及 | Bletilla formosana | 被子植物 | INSDC Sequences | |||
Lomariopsis 羅蔓藤蕨屬 | Lomariopsis boninensis | 蕨類 | 2020-07-05 | INSDC Sequences | ||
Salmonella enterica subsp. enterica serovar Newport | 2009-01-13 | INSDC Sequences | ||||
Papilio castor formosanus 無尾白紋鳳蝶(formosanus亞種) | Papilio castor formosanus | 蝶類 | 2006-04-06 | INSDC Sequences | ||
Leuconostoc pseudomesenteroides | 2012-06-06 | INSDC Sequences | ||||
Coenobita cavipes 凹足陸寄居蟹 | Coenobita cavipes | 蝦蟹類 | 2012-04-21 | INSDC Sequences | ||
Feline coronavirus | 2004-01-01 | INSDC Sequences | ||||
Enterovirus A71 | 2000-01-01 | INSDC Sequences | ||||
Hylarana latouchii 拉都希氏赤蛙 | Hylarana latouchii | 兩棲類 | INSDC Sequences | |||
Macrobrachium equidens 等齒沼蝦 | Macrobrachium equidens | 蝦蟹類 | INSDC Sequences | |||
Ceresium subuniforme 甲仙姬天牛 | Ceresium subuniforme | 甲蟲類 | 2008-05-24 | INSDC Sequences | ||
Luteochaete subglobosa | INSDC Sequences | |||||
Spencermartinsiella sp. W379 | 2011-01-20 | INSDC Sequences | ||||
Thunnus orientalis 太平洋黑鮪 | Thunnus orientalis | 魚類 | INSDC Sequences | |||
Amynthas amis 阿美遠環蚓 | Amynthas amis | 其他無脊椎 | INSDC Sequences | |||
Hommersandiophycus clavatus | 2002-04-26 | INSDC Sequences | ||||
Anourosorex yamashinai 短尾鼩 | Anourosorex yamashinai | 哺乳類 | INSDC Sequences | |||
Macrothele taiwanensis 臺灣長尾蛛 | Macrothele taiwanensis | 蜘蛛類 | INSDC Sequences | |||
Tetradium glabrifolium (Champ. ex Benth.) T.Hartley 賊仔樹 | Tetradium glabrifolium | 被子植物 | INSDC Sequences | |||
Entomortierella jenkinii | 2014-02-23 | INSDC Sequences | ||||
Leistus nokoensis | Leistus nokoensis | 甲蟲類 | 2010-12-02 | INSDC Sequences | ||
Nebria niitakana | Nebria niitakana | 甲蟲類 | 2010-08-03 | INSDC Sequences | ||
Thunnus tonggol 小黃鰭鮪 | Thunnus tonggol | 魚類 | INSDC Sequences | |||
Serranidae 鮨科 | Serranidae sp. ASIZP0078913 | 魚類 | INSDC Sequences | |||
Phytophthora 疫黴屬 | Phytophthora x incrassata | 原藻類 | 2013-01-01 | INSDC Sequences |