Open seltmann opened 3 years ago
@seltmann thanks for sharing your suggestion.
I produced the following table with the mycoportal data generously provided by @stbates @thebateslab for indexing by GloBI. I believe the dataset was a temporary substitute while maintenance was being done. As you can see, basis of record was not (yet) included in this data file.
If you have ideas for a better source of mycoportal data, please do share.
via
$ curl -L "https://github.com/globalbioticinteractions/mycoportal/raw/main/tmp_host_info-20200902.csv.gz"\
| gunzip\
| head\
| mlr --icsv --omd cat
the following markdown table was generated:
occid | sciname | country | locality | substrate | host | associatedtaxa | catalogNumber | collid |
---|---|---|---|---|---|---|---|---|
3042414 | United States | Populus balsamifera | CBRU00003514 | 54 | ||||
3043800 | Philippines | on N slope of Mt. Apo | Coleoptera: Staphylinidae | SYRF0007954 | 33 | |||
3043970 | RMS0004987 | 35 | ||||||
3044320 | RMS0005073 | 35 | ||||||
3050053 | RMS0005366 | 35 | ||||||
2854245 | United States | Greenhouse | Solanum tuberosum | CUP-029072 | 23 | |||
2854248 | United States | Pl. Path. Greenhouse | Lilium longiflorum giganteum | CUP-021618 | 23 | |||
2854252 | United States | potato tuber | Solanum tuberosum | CUP-029215 | 23 | |||
2854256 | Solanum tuberosum | CUP-012554 | 23 |
Now that the MycoPortal is back online, I switched to using the mycoportal rss feed instead of the intermediate data dump provided earlier.
With this, the basisOfRecord values are showing up.
For example, see 9 associations below extracted using:
elton update globalbioticinteractions/mycoportal
elton interactions | head | mlr --itsvlite --oxtab cat
yielding
argumentTypeId https://en.wiktionary.org/wiki/support
sourceOccurrenceId 02-01000548784
sourceCatalogNumber 76001
sourceCollectionCode DAOM
sourceCollectionId 88a2a8f6-98e7-4a34-8d2e-238ff4cff80a
sourceInstitutionCode AAFC-AAC
sourceTaxonId 85742
sourceTaxonName Aecidium alstroemeriae
sourceTaxonRank
sourceTaxonPathIds
sourceTaxonPath Fungi | Basidiomycota | Pucciniomycetes | Pucciniales | Pucciniaceae | Aecidium | Aecidium alstroemeriae
sourceTaxonPathNames kingdom | phylum | class | order | family | genus | species
sourceBodyPartId
sourceBodyPartName
sourceLifeStageId
sourceLifeStageName
sourceSexId
sourceSexName
interactionTypeId http://purl.obolibrary.org/obo/RO_0002454
interactionTypeName hasHost
targetOccurrenceId
targetCatalogNumber
targetCollectionCode
targetCollectionId
targetInstitutionCode
targetTaxonId
targetTaxonName Alstroemeria sp.
targetTaxonRank
targetTaxonPathIds
targetTaxonPath
targetTaxonPathNames
targetBodyPartId
targetBodyPartName
targetLifeStageId
targetLifeStageName
targetSexId
targetSexName
basisOfRecordId
basisOfRecordName PreservedSpecimen
http://rs.tdwg.org/dwc/terms/eventDate 1919-09-18T00:00:00Z
decimalLatitude
decimalLongitude
localityId
localityName Papudo
referenceDoi
referenceUrl https://www.mycoportal.org/portal/collections/individual/index.php?occid=11582868
referenceCitation https://www.mycoportal.org/portal/collections/individual/index.php?occid=11582868
namespace local
citation AAFC-AAC-DAOM DwC-Archive | Darwin Core Archive for Canadian National Mycological Herbarium
archiveURI https://www.mycoportal.org/portal/content/dwca/AAFC-AAC-DAOM_DwC-A.zip
lastSeenAt
contentHash
eltonVersion 0.12.11
argumentTypeId https://en.wiktionary.org/wiki/support
sourceOccurrenceId 02-01000548785
sourceCatalogNumber 6428
sourceCollectionCode DAOM
sourceCollectionId 88a2a8f6-98e7-4a34-8d2e-238ff4cff80a
sourceInstitutionCode AAFC-AAC
sourceTaxonId
sourceTaxonName Aecidium borricheae
sourceTaxonRank
sourceTaxonPathIds
sourceTaxonPath
sourceTaxonPathNames
sourceBodyPartId
sourceBodyPartName
sourceLifeStageId
sourceLifeStageName
sourceSexId
sourceSexName
interactionTypeId http://purl.obolibrary.org/obo/RO_0002454
interactionTypeName hasHost
targetOccurrenceId
targetCatalogNumber
targetCollectionCode
targetCollectionId
targetInstitutionCode
targetTaxonId
targetTaxonName Borrichia frutescens
targetTaxonRank
targetTaxonPathIds
targetTaxonPath
targetTaxonPathNames
targetBodyPartId
targetBodyPartName
targetLifeStageId
targetLifeStageName
targetSexId
targetSexName
basisOfRecordId
basisOfRecordName PreservedSpecimen
http://rs.tdwg.org/dwc/terms/eventDate 1901-04-27T00:00:00Z
decimalLatitude
decimalLongitude
localityId
localityName Fort Morgan
referenceDoi
referenceUrl https://www.mycoportal.org/portal/collections/individual/index.php?occid=11582879
referenceCitation https://www.mycoportal.org/portal/collections/individual/index.php?occid=11582879
namespace local
citation AAFC-AAC-DAOM DwC-Archive | Darwin Core Archive for Canadian National Mycological Herbarium
archiveURI https://www.mycoportal.org/portal/content/dwca/AAFC-AAC-DAOM_DwC-A.zip
lastSeenAt
contentHash
eltonVersion 0.12.11
argumentTypeId https://en.wiktionary.org/wiki/support
sourceOccurrenceId 02-01000548786
sourceCatalogNumber 3912
sourceCollectionCode DAOM
sourceCollectionId 88a2a8f6-98e7-4a34-8d2e-238ff4cff80a
sourceInstitutionCode AAFC-AAC
sourceTaxonId 85719
sourceTaxonName Aecidium ageratinae
sourceTaxonRank
sourceTaxonPathIds
sourceTaxonPath Fungi | Basidiomycota | Pucciniomycetes | Pucciniales | Pucciniaceae | Aecidium | Aecidium ageratinae
sourceTaxonPathNames kingdom | phylum | class | order | family | genus | species
sourceBodyPartId
sourceBodyPartName
sourceLifeStageId
sourceLifeStageName
sourceSexId
sourceSexName
interactionTypeId http://purl.obolibrary.org/obo/RO_0002454
interactionTypeName hasHost
targetOccurrenceId
targetCatalogNumber
targetCollectionCode
targetCollectionId
targetInstitutionCode
targetTaxonId
targetTaxonName Ageratina altissima
targetTaxonRank
targetTaxonPathIds
targetTaxonPath
targetTaxonPathNames
targetBodyPartId
targetBodyPartName
targetLifeStageId
targetLifeStageName
targetSexId
targetSexName
basisOfRecordId
basisOfRecordName PreservedSpecimen
http://rs.tdwg.org/dwc/terms/eventDate 1936-06-23T00:00:00Z
decimalLatitude
decimalLongitude
localityId
localityName Abbotsford
referenceDoi
referenceUrl https://www.mycoportal.org/portal/collections/individual/index.php?occid=11582850
referenceCitation https://www.mycoportal.org/portal/collections/individual/index.php?occid=11582850
namespace local
citation AAFC-AAC-DAOM DwC-Archive | Darwin Core Archive for Canadian National Mycological Herbarium
archiveURI https://www.mycoportal.org/portal/content/dwca/AAFC-AAC-DAOM_DwC-A.zip
lastSeenAt
contentHash
eltonVersion 0.12.11
argumentTypeId https://en.wiktionary.org/wiki/support
sourceOccurrenceId 02-01000548787
sourceCatalogNumber 76012
sourceCollectionCode DAOM
sourceCollectionId 88a2a8f6-98e7-4a34-8d2e-238ff4cff80a
sourceInstitutionCode AAFC-AAC
sourceTaxonId 85997
sourceTaxonName Aecidium chuquiraguae
sourceTaxonRank
sourceTaxonPathIds
sourceTaxonPath Fungi | Basidiomycota | Pucciniomycetes | Pucciniales | Pucciniaceae | Aecidium | Aecidium chuquiraguae
sourceTaxonPathNames kingdom | phylum | class | order | family | genus | species
sourceBodyPartId
sourceBodyPartName
sourceLifeStageId
sourceLifeStageName
sourceSexId
sourceSexName
interactionTypeId http://purl.obolibrary.org/obo/RO_0002454
interactionTypeName hasHost
targetOccurrenceId
targetCatalogNumber
targetCollectionCode
targetCollectionId
targetInstitutionCode
targetTaxonId
targetTaxonName Chuquiragua sp.
targetTaxonRank
targetTaxonPathIds
targetTaxonPath
targetTaxonPathNames
targetBodyPartId
targetBodyPartName
targetLifeStageId
targetLifeStageName
targetSexId
targetSexName
basisOfRecordId
basisOfRecordName PreservedSpecimen
http://rs.tdwg.org/dwc/terms/eventDate 1922-04-20T00:00:00Z
decimalLatitude
decimalLongitude
localityId
localityName Campos do Jordao
referenceDoi
referenceUrl https://www.mycoportal.org/portal/collections/individual/index.php?occid=11582887
referenceCitation https://www.mycoportal.org/portal/collections/individual/index.php?occid=11582887
namespace local
citation AAFC-AAC-DAOM DwC-Archive | Darwin Core Archive for Canadian National Mycological Herbarium
archiveURI https://www.mycoportal.org/portal/content/dwca/AAFC-AAC-DAOM_DwC-A.zip
lastSeenAt
contentHash
eltonVersion 0.12.11
argumentTypeId https://en.wiktionary.org/wiki/support
sourceOccurrenceId 02-01000548788
sourceCatalogNumber 76113
sourceCollectionCode DAOM
sourceCollectionId 88a2a8f6-98e7-4a34-8d2e-238ff4cff80a
sourceInstitutionCode AAFC-AAC
sourceTaxonId 102660
sourceTaxonName Arthuria catenulata
sourceTaxonRank
sourceTaxonPathIds
sourceTaxonPath Fungi | Basidiomycota | Pucciniomycetes | Pucciniales | Phakopsoraceae | Arthuria | Arthuria catenulata
sourceTaxonPathNames kingdom | phylum | class | order | family | genus | species
sourceBodyPartId
sourceBodyPartName
sourceLifeStageId
sourceLifeStageName
sourceSexId
sourceSexName
interactionTypeId http://purl.obolibrary.org/obo/RO_0002454
interactionTypeName hasHost
targetOccurrenceId
targetCatalogNumber
targetCollectionCode
targetCollectionId
targetInstitutionCode
targetTaxonId
targetTaxonName Croton? sp.
targetTaxonRank
targetTaxonPathIds
targetTaxonPath
targetTaxonPathNames
targetBodyPartId
targetBodyPartName
targetLifeStageId
targetLifeStageName
targetSexId
targetSexName
basisOfRecordId
basisOfRecordName PreservedSpecimen
http://rs.tdwg.org/dwc/terms/eventDate 1921-08-17T00:00:00Z
decimalLatitude
decimalLongitude
localityId
localityName Paineiras
referenceDoi
referenceUrl https://www.mycoportal.org/portal/collections/individual/index.php?occid=11583123
referenceCitation https://www.mycoportal.org/portal/collections/individual/index.php?occid=11583123
namespace local
citation AAFC-AAC-DAOM DwC-Archive | Darwin Core Archive for Canadian National Mycological Herbarium
archiveURI https://www.mycoportal.org/portal/content/dwca/AAFC-AAC-DAOM_DwC-A.zip
lastSeenAt
contentHash
eltonVersion 0.12.11
argumentTypeId https://en.wiktionary.org/wiki/support
sourceOccurrenceId 02-01000548789
sourceCatalogNumber 24393
sourceCollectionCode DAOM
sourceCollectionId 88a2a8f6-98e7-4a34-8d2e-238ff4cff80a
sourceInstitutionCode AAFC-AAC
sourceTaxonId 86400
sourceTaxonName Aecidium hornotinum
sourceTaxonRank
sourceTaxonPathIds
sourceTaxonPath Fungi | Basidiomycota | Pucciniomycetes | Pucciniales | Pucciniaceae | Aecidium | Aecidium hornotinum
sourceTaxonPathNames kingdom | phylum | class | order | family | genus | species
sourceBodyPartId
sourceBodyPartName
sourceLifeStageId
sourceLifeStageName
sourceSexId
sourceSexName
interactionTypeId http://purl.obolibrary.org/obo/RO_0002454
interactionTypeName hasHost
targetOccurrenceId
targetCatalogNumber
targetCollectionCode
targetCollectionId
targetInstitutionCode
targetTaxonId
targetTaxonName Meliosma affin. multiflora
targetTaxonRank
targetTaxonPathIds
targetTaxonPath
targetTaxonPathNames
targetBodyPartId
targetBodyPartName
targetLifeStageId
targetLifeStageName
targetSexId
targetSexName
basisOfRecordId
basisOfRecordName PreservedSpecimen
http://rs.tdwg.org/dwc/terms/eventDate 1935-03-26T00:00:00Z
decimalLatitude
decimalLongitude
localityId
localityName Mt. Sant Tomas
referenceDoi
referenceUrl https://www.mycoportal.org/portal/collections/individual/index.php?occid=11582941
referenceCitation https://www.mycoportal.org/portal/collections/individual/index.php?occid=11582941
namespace local
citation AAFC-AAC-DAOM DwC-Archive | Darwin Core Archive for Canadian National Mycological Herbarium
archiveURI https://www.mycoportal.org/portal/content/dwca/AAFC-AAC-DAOM_DwC-A.zip
lastSeenAt
contentHash
eltonVersion 0.12.11
argumentTypeId https://en.wiktionary.org/wiki/support
sourceOccurrenceId 02-01000548789
sourceCatalogNumber 24393
sourceCollectionCode DAOM
sourceCollectionId 88a2a8f6-98e7-4a34-8d2e-238ff4cff80a
sourceInstitutionCode AAFC-AAC
sourceTaxonId 86400
sourceTaxonName Aecidium hornotinum
sourceTaxonRank
sourceTaxonPathIds
sourceTaxonPath Fungi | Basidiomycota | Pucciniomycetes | Pucciniales | Pucciniaceae | Aecidium | Aecidium hornotinum
sourceTaxonPathNames kingdom | phylum | class | order | family | genus | species
sourceBodyPartId
sourceBodyPartName
sourceLifeStageId
sourceLifeStageName
sourceSexId
sourceSexName
interactionTypeId http://purl.obolibrary.org/obo/RO_0002220
interactionTypeName adjacentTo
targetOccurrenceId
targetCatalogNumber
targetCollectionCode
targetCollectionId
targetInstitutionCode
targetTaxonId
targetTaxonName leaves
targetTaxonRank
targetTaxonPathIds
targetTaxonPath
targetTaxonPathNames
targetBodyPartId
targetBodyPartName
targetLifeStageId
targetLifeStageName
targetSexId
targetSexName
basisOfRecordId
basisOfRecordName PreservedSpecimen
http://rs.tdwg.org/dwc/terms/eventDate 1935-03-26T00:00:00Z
decimalLatitude
decimalLongitude
localityId
localityName Mt. Sant Tomas
referenceDoi
referenceUrl https://www.mycoportal.org/portal/collections/individual/index.php?occid=11582941
referenceCitation https://www.mycoportal.org/portal/collections/individual/index.php?occid=11582941
namespace local
citation AAFC-AAC-DAOM DwC-Archive | Darwin Core Archive for Canadian National Mycological Herbarium
archiveURI https://www.mycoportal.org/portal/content/dwca/AAFC-AAC-DAOM_DwC-A.zip
lastSeenAt
contentHash
eltonVersion 0.12.11
argumentTypeId https://en.wiktionary.org/wiki/support
sourceOccurrenceId 02-01000548790
sourceCatalogNumber 20858
sourceCollectionCode DAOM
sourceCollectionId 88a2a8f6-98e7-4a34-8d2e-238ff4cff80a
sourceInstitutionCode AAFC-AAC
sourceTaxonId 86468
sourceTaxonName Aecidium ivae
sourceTaxonRank
sourceTaxonPathIds
sourceTaxonPath Fungi | Basidiomycota | Pucciniomycetes | Pucciniales | Pucciniaceae | Aecidium | Aecidium ivae
sourceTaxonPathNames kingdom | phylum | class | order | family | genus | species
sourceBodyPartId
sourceBodyPartName
sourceLifeStageId
sourceLifeStageName
sourceSexId
sourceSexName
interactionTypeId http://purl.obolibrary.org/obo/RO_0002454
interactionTypeName hasHost
targetOccurrenceId
targetCatalogNumber
targetCollectionCode
targetCollectionId
targetInstitutionCode
targetTaxonId
targetTaxonName Iva frutescens
targetTaxonRank
targetTaxonPathIds
targetTaxonPath
targetTaxonPathNames
targetBodyPartId
targetBodyPartName
targetLifeStageId
targetLifeStageName
targetSexId
targetSexName
basisOfRecordId
basisOfRecordName PreservedSpecimen
http://rs.tdwg.org/dwc/terms/eventDate 1907-08-14T00:00:00Z
decimalLatitude
decimalLongitude
localityId
localityName Lewes
referenceDoi
referenceUrl https://www.mycoportal.org/portal/collections/individual/index.php?occid=11582962
referenceCitation https://www.mycoportal.org/portal/collections/individual/index.php?occid=11582962
namespace local
citation AAFC-AAC-DAOM DwC-Archive | Darwin Core Archive for Canadian National Mycological Herbarium
archiveURI https://www.mycoportal.org/portal/content/dwca/AAFC-AAC-DAOM_DwC-A.zip
lastSeenAt
contentHash
eltonVersion 0.12.11
argumentTypeId https://en.wiktionary.org/wiki/support
sourceOccurrenceId 02-01000548791
sourceCatalogNumber 19341
sourceCollectionCode DAOM
sourceCollectionId 88a2a8f6-98e7-4a34-8d2e-238ff4cff80a
sourceInstitutionCode AAFC-AAC
sourceTaxonId 86539
sourceTaxonName Aecidium leonense
sourceTaxonRank
sourceTaxonPathIds
sourceTaxonPath Fungi | Basidiomycota | Pucciniomycetes | Pucciniales | Pucciniaceae | Aecidium | Aecidium leonense
sourceTaxonPathNames kingdom | phylum | class | order | family | genus | species
sourceBodyPartId
sourceBodyPartName
sourceLifeStageId
sourceLifeStageName
sourceSexId
sourceSexName
interactionTypeId http://purl.obolibrary.org/obo/RO_0002454
interactionTypeName hasHost
targetOccurrenceId
targetCatalogNumber
targetCollectionCode
targetCollectionId
targetInstitutionCode
targetTaxonId
targetTaxonName Dioscorea sp
targetTaxonRank
targetTaxonPathIds
targetTaxonPath
targetTaxonPathNames
targetBodyPartId
targetBodyPartName
targetLifeStageId
targetLifeStageName
targetSexId
targetSexName
basisOfRecordId
basisOfRecordName PreservedSpecimen
http://rs.tdwg.org/dwc/terms/eventDate 1940-04-26T00:00:00Z
decimalLatitude
decimalLongitude
localityId
localityName Sembehun
referenceDoi
referenceUrl https://www.mycoportal.org/portal/collections/individual/index.php?occid=11582967
referenceCitation https://www.mycoportal.org/portal/collections/individual/index.php?occid=11582967
namespace local
citation AAFC-AAC-DAOM DwC-Archive | Darwin Core Archive for Canadian National Mycological Herbarium
archiveURI https://www.mycoportal.org/portal/content/dwca/AAFC-AAC-DAOM_DwC-A.zip
lastSeenAt
contentHash
eltonVersion 0.12.11
@jhpoelen Please consider updating the GloBI import to include a sourceBasisOfRecordName. Presently 1,278,142 records from mycoportal.org do not include BasisOfRecord information. This would be useful for understanding what records in GloBI are coming from PreservedSpecimens or HumanObservations. Thanks!