associatedOccurrences format

[jhpoelen]

MCZ contains associatedOccurrences in the following format:

$ unzip -p mcz.zip occurrence.txt | cut -f30 | grep -P "collection_object_id" | grep "paras" | head
parasitically found on/in          <a href="http://mczbase.mcz.harvard.edu/SpecimenDetail.cfm?collection_object_id=5197872"> MCZ IZ ECH-8358</a>
parasitically found on/in          <a href="http://mczbase.mcz.harvard.edu/SpecimenDetail.cfm?collection_object_id=1563036"> MCZ Ich 47556</a>
brood parasitized by          <a href="http://mczbase.mcz.harvard.edu/SpecimenDetail.cfm?collection_object_id=3151006"> MCZ Orn 356498</a>
brood parasitized by          <a href="http://mczbase.mcz.harvard.edu/SpecimenDetail.cfm?collection_object_id=5259116"> MCZ Orn 364962</a>
brood parasitized by          <a href="http://mczbase.mcz.harvard.edu/SpecimenDetail.cfm?collection_object_id=3150971"> MCZ Orn 356528</a>
brood parasitized by          <a href="http://mczbase.mcz.harvard.edu/SpecimenDetail.cfm?collection_object_id=5256459"> MCZ Orn 364961</a>
brood parasitized by          <a href="http://mczbase.mcz.harvard.edu/SpecimenDetail.cfm?collection_object_id=3151012"> MCZ Orn 357077</a>
parasitically found on/in          <a href="http://mczbase.mcz.harvard.edu/SpecimenDetail.cfm?collection_object_id=3223947"> MCZ IZ CRI-117</a>
parasitically found on/in          <a href="http://mczbase.mcz.harvard.edu/SpecimenDetail.cfm?collection_object_id=2930518"> MCZ IZ CRU-8019</a>
parasitically found on/in          <a href="http://mczbase.mcz.harvard.edu/SpecimenDetail.cfm?collection_object_id=1446101"> MCZ Ich 722</a>

with semi-colons being separators for lists.

This is slightly different from the Arctos notation of (has parasite) [some occurrenceId], so GloBI does not yet understand how to link these records.

[jhpoelen]

More examples include:

$ unzip -p mcz.zip occurrence.txt | cut -f30 | grep -P "collection_object_id" | head
duplicate recataloged as          <a href="http://mczbase.mcz.harvard.edu/SpecimenDetail.cfm?collection_object_id=596800"> MCZ Herp R-84811</a>
bad duplicate of          <a href="http://mczbase.mcz.harvard.edu/SpecimenDetail.cfm?collection_object_id=3881801"> MCZ HerpOBS 1</a>
embryo of          <a href="http://mczbase.mcz.harvard.edu/SpecimenDetail.cfm?collection_object_id=4674447"> MCZ Herp A-152570</a>
from same lot as          <a href="http://mczbase.mcz.harvard.edu/SpecimenDetail.cfm?collection_object_id=666604"> MCZ Mamm 3186</a>; from same lot as          <a href="http://mczbase.mcz.harvard.edu/SpecimenDetail.cfm?collection_object_id=666606"> MCZ Mamm 3187</a>; from same lot as          <a href="http://mczbase.mcz.harvard.edu/SpecimenDetail.cfm?collection_object_id=666608"> MCZ Mamm 3188</a>; from same lot as          <a href="http://mczbase.mcz.harvard.edu/SpecimenDetail.cfm?collection_object_id=666610"> MCZ Mamm 3190</a>; from same lot as          <a href="http://mczbase.mcz.harvard.edu/SpecimenDetail.cfm?collection_object_id=666612"> MCZ Mamm 3192</a>; from same lot as          <a href="http://mczbase.mcz.harvard.edu/SpecimenDetail.cfm?collection_object_id=678406"> MCZ Mamm 3191</a>; from same lot as          <a href="http://mczbase.mcz.harvard.edu/SpecimenDetail.cfm?collection_object_id=730482"> MCZ Mamm 3189</a>
from same lot as          <a href="http://mczbase.mcz.harvard.edu/SpecimenDetail.cfm?collection_object_id=666610"> MCZ Mamm 3190</a>; from same lot as          <a href="http://mczbase.mcz.harvard.edu/SpecimenDetail.cfm?collection_object_id=666612"> MCZ Mamm 3192</a>; from same lot as          <a href="http://mczbase.mcz.harvard.edu/SpecimenDetail.cfm?collection_object_id=678406"> MCZ Mamm 3191</a>; from same lot as          <a href="http://mczbase.mcz.harvard.edu/SpecimenDetail.cfm?collection_object_id=730482"> MCZ Mamm 3189</a>
from same lot as          <a href="http://mczbase.mcz.harvard.edu/SpecimenDetail.cfm?collection_object_id=666612"> MCZ Mamm 3192</a>; from same lot as          <a href="http://mczbase.mcz.harvard.edu/SpecimenDetail.cfm?collection_object_id=678406"> MCZ Mamm 3191</a>
split into          <a href="http://mczbase.mcz.harvard.edu/SpecimenDetail.cfm?collection_object_id=3354186"> MCZ Mamm 6085</a>
cloned from record          <a href="http://mczbase.mcz.harvard.edu/SpecimenDetail.cfm?collection_object_id=677308"> MCZ Mamm 61712</a>
parent of          <a href="http://mczbase.mcz.harvard.edu/SpecimenDetail.cfm?collection_object_id=757389"> MCZ Mamm 35744</a>
cloned from record          <a href="http://mczbase.mcz.harvard.edu/SpecimenDetail.cfm?collection_object_id=677308"> MCZ Mamm 61712</a>

[jhpoelen]

After making various changes to the way GloBI links occurrences across, and within, datasets, the following sample was extracted from elton interactions globalbioticinteractions/mcz results:

argumentTypeId	sourceOccurrenceId	sourceCatalogNumber	sourceCollectionCode	sourceCollectionId	sourceInstitutionCode	sourceTaxonId	sourceTaxonName	sourceTaxonRank	sourceTaxonPathIds	sourceTaxonPath	sourceTaxonPathNames	sourceBodyPartId	sourceBodyPartName	sourceLifeStageId	sourceLifeStageName	sourceSexId	sourceSexName	interactionTypeId	interactionTypeName	targetOccurrenceId	targetCatalogNumber	targetCollectionCode	targetCollectionId	targetInstitutionCode	targetTaxonId	targetTaxonName	targetTaxonRank	targetTaxonPathIds	targetTaxonPath	targetTaxonPathNames	targetBodyPartId	targetBodyPartName	targetLifeStageId	targetLifeStageName	targetSexId	targetSexName	basisOfRecordId	basisOfRecordName	http://rs.tdwg.org/dwc/terms/eventDate	decimalLatitude	decimalLongitude	localityId	localityName	referenceDoi	referenceUrl	referenceCitation	namespace	citation	archiveURI	lastSeenAt	contentHash	eltonVersion
https://en.wiktionary.org/wiki/support	MCZ:Mamm:61296	61296	Mamm		MCZ		Grampus griseus			Animalia | Chordata | Mammalia | Cetacea | Delphinidae | Grampus | Grampus griseus	kingdom | phylum | class | order | family | genus | species						male	http://purl.obolibrary.org/obo/RO_0008506	coOccursWith	MCZ:Mamm:61297	61297	Mamm		MCZ		Grampus griseus			Animalia | Chordata | Mammalia | Cetacea | Delphinidae | Grampus | Grampus griseus	kingdom | phylum | class | order | family | genus | species						male		PreservedSpecimen	1993-11-20T00:00:00Z	41.795942	-70.016129		Orleans, Skaket Beach		http://mczbase.mcz.harvard.edu/guid/MCZ:Mamm:61296	http://mczbase.mcz.harvard.edu/guid/MCZ:Mamm:61296	local	Museum of Comparative Zoology, Harvard University - Version 162.259	http://digir.mcz.harvard.edu/ipt/archive.do?r=mczbase			0.3.5-SNAPSHOT

The claim supports a claim in which two Risso's dolphins (Grampus griseus, http://mczbase.mcz.harvard.edu/guid/MCZ:Mamm:61296 and http://mczbase.mcz.harvard.edu/guid/MCZ:Mamm:61297) co-occurred at Orleans, Skaket Beach on 1993-11-20 . On closer inspection, the relations document a mass stranding of dolphins at Cape Cod on the Massachusetts coast.