global biotic interactions 物种交互数据库

[anneng]

globalbioticinteractions.org　这个数据记录了所有可以发现的物种之间的交互　包括吃与被吃　是否存在感染　我们可以提前其中的感染关系来找出人的病原体　构建一个数据库
通过下面的接口　可以查询出来所有支持的关系
https://api.globalbioticinteractions.org/interactionTypes

{"eats":{"source":"consumer","target":"food","termIRI":"http://purl.obolibrary.org/obo/RO_0002470"},"eatenBy":{"source":"food","target":"consumer","termIRI":"http://purl.obolibrary.org/obo/RO_0002471"},"preysOn":{"source":"predator","target":"prey","termIRI":"http://purl.obolibrary.org/obo/RO_0002439"},"preyedUponBy":{"source":"prey","target":"predator","termIRI":"http://purl.obolibrary.org/obo/RO_0002458"},"kills":{"source":"killer","target":"victim","termIRI":"http://purl.obolibrary.org/obo/RO_0002626"},"killedBy":{"source":"victim","target":"killer","termIRI":"http://purl.obolibrary.org/obo/RO_0002627"},"parasiteOf":{"source":"parasite","target":"host","termIRI":"http://purl.obolibrary.org/obo/RO_0002444"},"hasParasite":{"source":"host","target":"parasite","termIRI":"http://purl.obolibrary.org/obo/RO_0002445"},"endoparasiteOf":{"source":"endoparasite","target":"host","termIRI":"http://purl.obolibrary.org/obo/RO_0002634"},"hasEndoparasite":{"source":"host","target":"endoparasite","termIRI":"http://purl.obolibrary.org/obo/RO_0002635"},"ectoparasiteOf":{"source":"ectoparasite","target":"host","termIRI":"http://purl.obolibrary.org/obo/RO_0002632"},"hasEctoparasite":{"source":"host","target":"ectoparasite","termIRI":"http://purl.obolibrary.org/obo/RO_0002633"},"parasitoidOf":{"source":"parasitoid","target":"host","termIRI":"http://purl.obolibrary.org/obo/RO_0002208"},"hasParasitoid":{"source":"host","target":"parasitoid","termIRI":"http://purl.obolibrary.org/obo/RO_0002209"},"hostOf":{"source":"host","target":"symbiont","termIRI":"http://purl.obolibrary.org/obo/RO_0002453"},"hasHost":{"source":"symbiont","target":"host","termIRI":"http://purl.obolibrary.org/obo/RO_0002454"},"pollinates":{"source":"pollinator","target":"plant","termIRI":"http://purl.obolibrary.org/obo/RO_0002455"},"pollinatedBy":{"source":"plant","target":"pollinator","termIRI":"http://purl.obolibrary.org/obo/RO_0002456"},"pathogenOf":{"source":"pathogen","target":"host","termIRI":"http://purl.obolibrary.org/obo/RO_0002556"},"hasPathogen":{"source":"host","target":"pathogen","termIRI":"http://purl.obolibrary.org/obo/RO_0002557"},"vectorOf":{"source":"vector","target":"pathogen","termIRI":"http://purl.obolibrary.org/obo/RO_0002459"},"hasVector":{"source":"pathogen","target":"vector","termIRI":"http://purl.obolibrary.org/obo/RO_0002460"},"dispersalVectorOf":{"source":"vector","target":"seed","termIRI":"no:match"},"hasDispersalVector":{"source":"seed","target":"vector","termIRI":"no:match"},"symbiontOf":{"source":"symbiont","target":"symbiont","termIRI":"http://purl.obolibrary.org/obo/RO_0002440"},"mutualistOf":{"source":"mutualist","target":"mutualist","termIRI":"http://purl.obolibrary.org/obo/RO_0002442"},"commensalistOf":{"source":"commensalist","target":"commensalist","termIRI":"http://purl.obolibrary.org/obo/RO_0002441"},"flowersVisitedBy":{"source":"plant","target":"visitor","termIRI":"http://purl.obolibrary.org/obo/RO_0002623"},"visitsFlowersOf":{"source":"visitor","target":"plant","termIRI":"http://purl.obolibrary.org/obo/RO_0002622"},"ecologicallyRelatedTo":{"source":"source","target":"target","termIRI":"http://purl.obolibrary.org/obo/RO_0002321"},"coOccursWith":{"source":"source","target":"target","termIRI":"http://purl.obolibrary.org/obo/RO_0008506"},"coRoostsWith":{"source":"source","target":"target","termIRI":"http://purl.obolibrary.org/obo/RO_0002801"},"interactsWith":{"source":"source","target":"target","termIRI":"http://purl.obolibrary.org/obo/RO_0002437"}}

[anneng]

https://www.globalbioticinteractions.org/data

下载sqlite数据库版本
gunzip interactions.csv.gz
cat interactions.csv | sqlite3 -csv globi.db '.import /dev/stdin interactions'

select count(*) from (select sourceTaxonName,interactionTypeName,targetTaxonName from interactions where targetTaxonName='Homo sapiens' and (interactionTypeName='pathogenOf' or interactionTypeName='endoparasiteOf' or interactionTypeName='hasHost' or interactionTypeName='parasiteOf' or interactionTypeName='ectoparasiteOf' or interactionTypeName='parasitoidOf') group by sourceTaxonName) as temp;

当前大概有1万多个病原

[anneng]

sqlite3

.open globi.db
.tables

[anneng]

导出数据：
sqlite> .headers on
sqlite> .mode csv
sqlite> .output data.csv
sqlite> SELECT customerid,
...> firstname,
...> lastname,
...> company
...> FROM customers;
sqlite> .quit