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 | |
---|---|---|---|---|---|---|
Bembidion teradai | Bembidion teradai | 甲蟲類 | 南投縣仁愛鄉 | INSDC Sequences | ||
Staphylococcus aureus | 2022-06-01 | 台中市和平區 | INSDC Sequences | |||
Murina gracilis 姬管鼻蝠 | Murina gracilis | 哺乳類 | 2009-08-12 | 花蓮縣秀林鄉 | INSDC Sequences | |
Leistus nokoensis | Leistus nokoensis | 甲蟲類 | 台中市和平區 | INSDC Sequences | ||
Staphylococcus aureus | 2022-06-01 | 台中市和平區 | INSDC Sequences | |||
Ectoedemia sp. Quercus tatakaensis TW | 2012-10-11 | 花蓮縣秀林鄉 | INSDC Sequences | |||
Nebria formosana | Nebria formosana | 甲蟲類 | 台中市和平區 | INSDC Sequences | ||
Staphylococcus aureus | 2022-06-01 | 台中市和平區 | INSDC Sequences | |||
Ectoedemia sp. Quercus tatakaensis TW | 2012-10-11 | 花蓮縣秀林鄉 | INSDC Sequences | |||
Leistus smetanai | Leistus smetanai | 甲蟲類 | 台中市和平區 | INSDC Sequences | ||
Staphylococcus aureus | 2022-06-01 | 台中市和平區 | INSDC Sequences | |||
Nebria niitakana | Nebria niitakana | 甲蟲類 | 台中市和平區 | INSDC Sequences | ||
Staphylococcus aureus | 2022-06-01 | 台中市和平區 | INSDC Sequences | |||
Ectoedemia sp. Rosa Taiwan | 2012-10-11 | 花蓮縣秀林鄉 | INSDC Sequences | |||
Ectoedemia sp. Rubus Taiwan | 2012-10-10 | 宜蘭縣大同鄉 | INSDC Sequences | |||
Bombus trifasciatus 威氏熊蜂 | Bombus trifasciatus | 其他昆蟲 | 南投縣仁愛鄉 | INSDC Sequences | ||
Meretrix lamarckii 韓國文蛤 | Meretrix lamarckii | 蝸牛與貝類 | 2018-07-09 | 金門縣金湖鎮 | INSDC Sequences | |
Nephius sp. CNCCOLVG00006717 | 2013-08-11 | 台中市和平區 | INSDC Sequences | |||
Euthycus | Euthycus sp. CNCCOLVG00006683 | 甲蟲類 | 2013-08-11 | 台中市和平區 | INSDC Sequences | |
Culicoides 庫蠓屬 | Culicoides nudipalpis | 其他昆蟲 | 1995-09-20 | 金門縣金湖鎮 | INSDC Sequences | |
Nasutitermes 象白蟻屬 | Nasutitermes kinoshitai | 其他昆蟲 | 2014-04-02 | 桃園市復興區 | INSDC Sequences | |
Phanerochaete | Phanerochaete sp. | 真菌類 | 2008-05-22 | 台中市和平區 | INSDC Sequences | |
Scolopocryptops curtus 短棘盲蜈蚣 | Scolopocryptops curtus | 其他無脊椎 | 2019-03-19 | 苗栗縣泰安鄉 | INSDC Sequences | |
Nephius sp. CNCCOLVG00006719 | 2013-08-11 | 台中市和平區 | INSDC Sequences | |||
Microtropis fokienensis Dunn 福建賽衛矛 | Microtropis fokienensis | 被子植物 | 1997-11-01 | 苗栗縣泰安鄉 | INSDC Sequences |