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 | |
---|---|---|---|---|---|---|
Streptococcus dysgalactiae | 2008-01-01 | INSDC Sequences | ||||
Halobacillus trueperi | 2013-07-08 | INSDC Sequences | ||||
Magnolia 木蘭屬 | Magnolia compressa | 被子植物 | INSDC Sequences | |||
Gymnothorax formosus 美麗裸胸鯙 | Gymnothorax formosus | 魚類 | INSDC Sequences | |||
Nebria uenoiana | Nebria uenoiana | 甲蟲類 | 2011-12-08 | INSDC Sequences | ||
Nebria uenoiana | Nebria uenoiana | 甲蟲類 | 2011-09-03 | INSDC Sequences | ||
Trichiurus japonicus 日本帶魚 | Trichiurus japonicus | 魚類 | INSDC Sequences | |||
Diodon holocanthus 六斑二齒魨 | Diodon holocanthus | 魚類 | INSDC Sequences | |||
Amynthas 遠環蚓屬 | Amynthas sp. 1 SCC-2015 | 其他無脊椎 | INSDC Sequences | |||
Phytophthora 疫黴屬 | Phytophthora x heterohybrida | 原藻類 | 2013-01-01 | INSDC Sequences | ||
Mandarella flaviventris 黃腹瘦葉蚤 | Mandarella flaviventris | 甲蟲類 | INSDC Sequences | |||
Anopheles 瘧蚊屬 | Anopheles lindesayi | 其他昆蟲 | 2016-08-22 | INSDC Sequences | ||
Enicospilus 細顎姬蜂屬 | Enicospilus sp. SS-2019H | 其他昆蟲 | 2015-10-04 | INSDC Sequences | ||
Cephalotaxus 粗榧屬 | Cephalotaxus harringtonia var. wilsoniana | 裸子植物 | 2020-04-01 | INSDC Sequences | ||
Cylindera | Cylindera subtilis | 甲蟲類 | 2020-07-11 | INSDC Sequences | ||
Ursus thibetanus formosanus 臺灣黑熊 | Ursus thibetanus formosanus | 哺乳類 | INSDC Sequences | |||
Pieris rapae 白粉蝶 | Pieris rapae | 蝶類 | 2016-02-10 | INSDC Sequences | ||
Caulerpa 蕨藻屬 | Caulerpa cupressoides var. mamillosa | INSDC Sequences | ||||
Dendriscosticta 樹牛皮葉衣屬 | Dendriscosticta aff. hookeri | 真菌類 | INSDC Sequences | |||
Gaertneriomyces 狀哥德納壺菌屬 | Gaertneriomyces spectabilis | 真菌類 | 1992-07-22 | INSDC Sequences | ||
Lomariopsis 羅蔓藤蕨屬 | Lomariopsis boninensis | 蕨類 | 2021-03-28 | INSDC Sequences | ||
Geothelphusa olea 黃綠澤蟹 | Geothelphusa olea | 蝦蟹類 | 1988-09-10 | INSDC Sequences | ||
Leuconostoc mesenteroides | 2010-08-27 | INSDC Sequences | ||||
Lactiplantibacillus plantarum | 2011-07-07 | INSDC Sequences | ||||
Orthetrum pruinosum 霜白蜻蜓 | Orthetrum pruinosum | 蜻蛉類 | 2011-06-29 | INSDC Sequences |