jhpoelen edited this page Sep 6, 2018 · 13 revisions

This page provides some examples on how to access GloBI using neo4j's cypher query services. GloBI hosts a neo4j server instance that is publicly accessible, so you have a flexible way to query species interaction data. Here's some examples of such queries using the GloBI neo4j instance: http://tinyurl.com/whatthingsdohumanseat or http://tinyurl.com/whatthingsdotunaeat. Alternatives to accessing the GloBI species interaction data can be found here. If you have any questions about using the GloBI cypher query interface, please open an issue.

Cypher / REST query examples

Find mammals eaten by Homo sapiens in coastal areas.

Copy / paste cypher query below in Cypher Data Explorer. See issue #19 for more information.

START predatorTaxon = node:taxons(name='Homo sapiens'), preyTaxon = node:taxonPaths('path:Mammalia'),envo = node:environments('*:*') MATCH predatorTaxon<-[:CLASSIFIED_AS]-predator-[:ATE]->prey-[:CLASSIFIED_AS]->preyTaxon<-[:CLASSIFIED_AS]-pred2-[:ATE]->prey2-[:CLASSIFIED_AS]->preyOfPreyTaxon, predator-[:COLLECTED_AT]->location-[:HAS_ENVIRONMENT]->envo
WHERE envo.name = 'coast' RETURN envo.externalId, envo.name, preyTaxon.commonNames?, preyTaxon.path?, predatorTaxon.name as predatorName, preyTaxon.name as preyName, count(distinct preyOfPreyTaxon.name) as preyOfPreyCount

List first 10 prey taxa for predator Syacium papillosum

Look up first 10 distinct prey taxons for predator specimens that were classified as Syacium papillosum and matched against external taxonomy.

Execute query using cURL

curl -X POST -H Accept:application/json -H Content-Type:application/json -d '{"query": "START taxon = node:taxons(name=\"Syacium papillosum\") MATCH taxon<-[x:CLASSIFIED_AS]-predatorSpecimen-[:ATE]->preySpecimen-[:CLASSIFIED_AS]->preyTaxon where has(preyTaxon.externalId) and has(taxon.externalId) RETURN distinct preyTaxon.externalId as preyTaxonId, taxon.externalId as predatorTaxonId LIMIT 10"}' -v https://neo4j.globalbioticinteractions/db/data/ext/CypherPlugin/graphdb/execute_query

Example JSON response

{ "data" : [ [ "NCBITaxon:292503", "NCBITaxon:195649" ], [ "NCBITaxon:6805", "NCBITaxon:195649" ], [ "NCBITaxon:150701", "NCBITaxon:195649" ], [ "urn:lsid:marinespecies.org:taxname:101467", "NCBITaxon:195649" ], [ "NCBITaxon:111522", "NCBITaxon:195649" ], [ "NCBITaxon:338195", "NCBITaxon:195649" ], [ "urn:lsid:marinespecies.org:taxname:158021", "NCBITaxon:195649" ], [ "urn:lsid:marinespecies.org:taxname:118287", "NCBITaxon:195649" ], [ "urn:lsid:marinespecies.org:taxname:158368", "NCBITaxon:195649" ], [ "NCBITaxon:6810", "NCBITaxon:195649" ] ], "columns" : [ "preyTaxonId", "predatorTaxonId" ] }

List instigator taxon, interaction type, and target taxon for Adalia bipunctata

Copy and paste the Cypher query into http://tinyurl.com/whatthingsdohumanseat to reproduce results.

Example Cypher query

START study = node:studies('*:*') MATCH study-[:COLLECTED]->source-[:CLASSIFIED_AS]->sourceTaxon, source-[rel:ATE|PREYS_UPON|PARASITE_OF|HAS_HOST|INTERACTS_WITH]->target-[:CLASSIFIED_AS]->targetTaxon WHERE sourceTaxon.name = "Adalia bipunctata" RETURN  id(source) as sourceOccurrenceId, sourceTaxon.externalId, sourceTaxon.name, id(rel) as occurrenceInteractionId, type(rel) as occurrenceInteractionType, id(target) as targetOccurrenceId, targetTaxon.externalId, targetTaxon.name

Example result

==> | sourceOccurrenceId | sourceTaxon.externalId | sourceTaxon.name    | occurrenceInteractionId | occurrenceInteractionType | targetOccurrenceId | targetTaxon.externalId                | targetTaxon.name               |
==> +-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
==> | 881982             | "EOL:1174823"          | "Adalia bipunctata" | 220187                  | "PARASITE_OF"             | 881983             | "urn:lsid:bioinfo.org.uk:taxa:157663" | "Podapolipus"                  |
==> | 881980             | "EOL:1174823"          | "Adalia bipunctata" | 220182                  | "PARASITE_OF"             | 881981             | "urn:lsid:bioinfo.org.uk:taxa:157663" | "Podapolipus"                  |
==> | 881973             | "EOL:1174823"          | "Adalia bipunctata" | 220167                  | "INTERACTS_WITH"          | 881974             | "urn:lsid:bioinfo.org.uk:taxa:157662" | "Tetrastichus coccinellae"     |
==> | 881910             | "EOL:1174823"          | "Adalia bipunctata" | 220022                  | "INTERACTS_WITH"          | 881911             | "urn:lsid:bioinfo.org.uk:taxa:91775"  | "Phalacrotophora fasciata"     |
==> | 881892             | "EOL:1174823"          | "Adalia bipunctata" | 219977                  | "INTERACTS_WITH"          | 881893             | "urn:lsid:bioinfo.org.uk:taxa:102934" | "Phalacrotophora berolinensis" |
==> | 881877             | "EOL:1174823"          | "Adalia bipunctata" | 219942                  | "INTERACTS_WITH"          | 881879             | "urn:lsid:bioinfo.org.uk:taxa:102934" | "Phalacrotophora berolinensis" |
==> | 881859             | "EOL:1174823"          | "Adalia bipunctata" | 219902                  | "INTERACTS_WITH"          | 881860             | "urn:lsid:bioinfo.org.uk:taxa:91775"  | "Phalacrotophora fasciata"     |
==> +-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+

Even more examples

Total number of specimens collected across all studies

curl -X POST -H Accept:application/json -H Content-Type:application/json -d '{"query": "START study = node:studies(\"*:*\") MATCH study-[:COLLECTED]->specimen RETURN count(specimen)"}' -v https://neo4j.globalbioticinteractions.org/db/data/ext/CypherPlugin/graphdb/execute_query

Total number of classifications made across all studies

curl -X POST -H Accept:application/json -H Content-Type:application/json -d '{"query": "START study = node:studies(\"*:*\") MATCH study-[:COLLECTED]->specimen-[predatorClassifications:CLASSIFIED_AS]->taxon RETURN count(predatorClassifications)"}' -v https://neo4j.globalbioticinteractions.org/db/data/ext/CypherPlugin/graphdb/execute_query

Total number of predator specimens that were classified as taxon matched against external taxonomy

curl -X POST -H Accept:application/json -H Content-Type:application/json -d '{"query": "START study = node:studies(\"*:*\") MATCH study-[:COLLECTED]->specimen-[:CLASSIFIED_AS]->taxon WHERE has(taxon.externalId) RETURN count(specimen)"}' -v https://neo4j.globalbioticinteractions.org/db/data/ext/CypherPlugin/graphdb/execute_query

List of predator taxon names that did not match against an external taxonomy (with source-study reference)

curl -X POST -H Accept:application/json -H Content-Type:application/json -d '{"query": "START study = node:studies(\"*:*\") MATCH study-[:COLLECTED]->specimen-[:CLASSIFIED_AS]->taxon WHERE taxon.externalId = \"no:match\" RETURN distinct taxon.name, study.title"}' -v https://neo4j.globalbioticinteractions.org/db/data/ext/CypherPlugin/graphdb/execute_query

List of distinct predator names from a specific list of studies

START study = node:studies('*:*')
MATCH study-[:COLLECTED]->predator-[:CLASSIFIED_AS]->predatorTaxon
WHERE study.title in ['BAREMORE_ANGEL_SHARK','BARNES','simons/mississippiAlabamaFishDiet.csv.gz','akinMadIsland','Blewett2000CharlotteHarborFL','wrast/lavacaBayTrophicData.csv.gz']
RETURN distinct(predatorTaxon.name)

Produces a result such as:

"Caranx hippos"
"Syacium gunteri"
"Gadus morhua"
"Zalieutes mcgintyi"
"Clupea harengus"
...
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