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 | |
---|---|---|---|---|---|---|
Culicoides 庫蠓屬 | Culicoides tainanus | 其他昆蟲 | 1995-09-01 | 新北市三峽區 | INSDC Sequences | |
Favites pentagona 五邊角菊珊瑚 | Favites pentagona | 其他無脊椎 | 2015-08-03 | 台北市松山區 | INSDC Sequences | |
Culicoides 庫蠓屬 | Culicoides actoni | 其他昆蟲 | 1995-07-21 | 新北市三峽區 | INSDC Sequences | |
Paragoniastrea australensis 澳洲角星珊瑚 | Paragoniastrea australensis | 其他無脊椎 | 2016-08-21 | 台北市松山區 | INSDC Sequences | |
Paragoniastrea australensis 澳洲角星珊瑚 | Paragoniastrea australensis | 其他無脊椎 | 2016-08-19 | 台北市松山區 | INSDC Sequences | |
Favites pentagona 五邊角菊珊瑚 | Favites pentagona | 其他無脊椎 | 2014-07-18 | 台北市松山區 | INSDC Sequences | |
Bathynomus 大王具足蟲屬 | Bathynomus doederleinii | 蝦蟹類 | 2021-08-23 | 宜蘭縣頭城鎮 | INSDC Sequences | |
Favites pentagona 五邊角菊珊瑚 | Favites pentagona | 其他無脊椎 | 2015-08-02 | 台北市松山區 | INSDC Sequences | |
Astrea curta 簡短圓菊珊瑚 | Astrea curta | 其他無脊椎 | 2014-07-15 | 台北市松山區 | INSDC Sequences | |
Parapercis lutevittata 沙鱸 | Parapercis lutevittata | 魚類 | 2009-05-06 | 宜蘭縣頭城鎮 | INSDC Sequences | |
Dipsastraea favus 正菊珊瑚 | Dipsastraea favus | 其他無脊椎 | 2016-08-21 | 台北市松山區 | INSDC Sequences | |
Platygyra ryukyuensis 琉球腦紋珊瑚 | Platygyra ryukyuensis | 其他無脊椎 | 2016-07-28 | 台北市松山區 | INSDC Sequences | |
Bathynomus 大王具足蟲屬 | Bathynomus doederleinii | 蝦蟹類 | 2021-08-23 | 宜蘭縣頭城鎮 | INSDC Sequences | |
Favites 角菊珊瑚屬 | Favites stylifera | 其他無脊椎 | 2016-08-19 | 台北市松山區 | INSDC Sequences | |
Platygyra daedalea 大腦紋珊瑚 | Platygyra daedalea | 其他無脊椎 | 2016-08-19 | 台北市松山區 | INSDC Sequences | |
Favites pentagona 五邊角菊珊瑚 | Favites pentagona | 其他無脊椎 | 2014-07-18 | 台北市松山區 | INSDC Sequences | |
Platygyra 腦紋珊瑚屬 | Platygyra verweyi | 其他無脊椎 | 2016-08-21 | 台北市松山區 | INSDC Sequences | |
Stylophora pistillata 萼形柱珊瑚 | Stylophora pistillata | 其他無脊椎 | 2009-01-01 | 台北市松山區 | INSDC Sequences | |
Mycedium robokaki 小斜花珊瑚 | Mycedium robokaki | 其他無脊椎 | 2014-08-17 | 台北市松山區 | INSDC Sequences | |
Favites pentagona 五邊角菊珊瑚 | Favites pentagona | 其他無脊椎 | 2015-08-03 | 台北市松山區 | INSDC Sequences | |
Favites pentagona 五邊角菊珊瑚 | Favites pentagona | 其他無脊椎 | 2015-08-03 | 台北市松山區 | INSDC Sequences | |
Platygyra ryukyuensis 琉球腦紋珊瑚 | Platygyra ryukyuensis | 其他無脊椎 | 2014-08-16 | 台北市松山區 | INSDC Sequences | |
Favites pentagona 五邊角菊珊瑚 | Favites pentagona | 其他無脊椎 | 2014-07-18 | 台北市松山區 | INSDC Sequences | |
Favites 角菊珊瑚屬 | Favites stylifera | 其他無脊椎 | 2014-08-19 | 台北市松山區 | INSDC Sequences | |
Stylophora pistillata 萼形柱珊瑚 | Stylophora pistillata | 其他無脊椎 | 2009-01-01 | 台北市松山區 | INSDC Sequences |