Releases: globalbioticinteractions/globalbioticinteractions
Releases · globalbioticinteractions/globalbioticinteractions
v0.26.5
v0.26.4
Features
n/a
Improvements
- add support for rootparasite_of http://purl.obolibrary.org/obo/RO_000… …2236; related to #993 (comment)
- towards making workdir configurable; related to #999
Bug fixes
n/a
v0.26.2
Features
n/a
Improvements
- improve separated values in table cell values; #982
- skip BOM when reading csv/tsv files; related to #992
- remove substitution of source doi/urls on reference level to prevent … …sticky study citation seen in #992
- add support for http://purl.obolibrary.org/obo/RO_0002555 (allelopath… … of) related to #993 (comment)
- upgrade to Poelen, J. H. (2024). Global Biotic Interactions: Taxon Gr… …aph hash://sha256/5f5213f691969481aa349f0726a19bf5466dcdfd5a6223c71488ff2d48e01683 hash://md5/daee82c37dc0503a87d78ecdb80608d1 (0.5.2) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.12724138
- disable uri normalization in httpclient; related to #997
- allow for RO_ prefix in addition to RO: prefixes
Bug fixes
n/a
v0.26.1
Features
n/a
Improvements
- update globi taxon graph 0.4.5-> 0.4.6
- add support for separated values in CSV meta table definition. For example see https://github.com/globalbioticinteractions/globalbioticinteractions/blob/b5259582794568ca78077412cf694b9ba51ed3a9/eol-globi-data-sources/src/test/resources/org/eol/globi/data/test-meta-globi-separator.json
Example below, with special focus on separator field in the Sequences column.
{
"@context": [
"http://www.w3.org/ns/csvw",
{
"@language": "en"
}
],
"rdfs:comment": [
"inspired by https://www.w3.org/TR/2015/REC-tabular-data-model-20151217/"
],
"tables": [
{
"@context": [
"http://www.w3.org/ns/csvw",
{
"@language": "en"
}
],
"rdfs:comment": [
"inspired by https://www.w3.org/TR/2015/REC-tabular-data-model-20151217/"
],
"url": "https://figshare.com/ndownloader/files/2196534",
"dcterms:bibliographicCitation": "Wardeh, M., Risley, C., McIntyre, M. et al. Database of host-pathogen and related species interactions, and their global distribution. Sci Data 2, 150049 (2015). https://doi.org/10.1038/sdata.2015.49",
"delimiter": ",",
"headerRowCount": 1,
"interactionTypeName": "hasHost",
"interactionTypeId": "http://purl.obolibrary.org/obo/RO_0002454",
"null": [
""
],
"tableSchema": {
"columns": [
{
"name": "sourceTaxonName",
"titles": "Cargo",
"datatype": "string"
},
{
"name": "Cargo classification",
"titles": "Cargo classification",
"datatype": "string"
},
{
"name": "targetTaxonName",
"titles": "Carrier",
"datatype": "string"
},
{
"name": "Carrier classification",
"titles": "Carrier classification",
"datatype": "string"
},
{
"name": "Sequences count",
"titles": "Sequences count",
"datatype": "string"
},
{
"name": "Publications count",
"titles": "Publications count",
"datatype": "string"
},
{
"name": "referenceUrl",
"titles": "Sequences",
"separator": ";",
"datatype": {
"base": "string",
"valueUrl": "https://www.ncbi.nlm.nih.gov/nuccore/{referenceUrl}"
}
},
{
"name": "Publications",
"titles": "Publications",
"datatype": "string"
}
]
}
}
]
}
Bug fixes
n/a
v0.26.0
Features
- allow for linking of tables via primary/foreign keys in a globi.json schema definition. Inspired by #982 as well as many other datasets that split their interaction data across different tables (e.g., links, taxonomy, references) instead of providing a wide table that contains all information in a single row.
In the example below, a json configuration (note the primaryKey and foreignKeys parts) is shown that links resource/consumer (taxa) and reference id in a three column metaweb table to their associated data in taxonomy and reference tables.
{
"@context": [
"http://www.w3.org/ns/csvw",
{
"@language": "en"
}
],
"rdfs:comment": [
"inspired by https://www.w3.org/TR/2015/REC-tabular-data-model-20151217/"
],
"resources": {
"xlsx:https://datadryad.org/stash/downloads/file_stream/3078242!/Reference": "references.tsv",
"xlsx:https://datadryad.org/stash/downloads/file_stream/3078242!/Metaweb": "metaweb.tsv",
"xlsx:https://datadryad.org/stash/downloads/file_stream/3078242!/Node%20Taxonomy": "taxonomy.tsv"
},
"tables": [
{
"dcterms:bibliographicCitation": "Adhurya, Sagar; Lee, Da-Yeong; Park, Young-Seuk (2024). KF-metaweb: A trophic metaweb of freshwater ecosystems of South Korea (Version 1.0) [Dataset]. Dryad. https://doi.org/10.5061/dryad.cz8w9gjbc",
"url": "xlsx:https://datadryad.org/stash/downloads/file_stream/3078242!/Reference",
"headerRowCount": 1,
"delimiter": "\t",
"null": [
"NULL",
""
],
"tableSchema": {
"columns": [
{
"name": "referenceId",
"titles": "Reference number",
"datatype": "string"
},
{
"name": "referenceCitation",
"titles": "Reference",
"datatype": "string"
}
],
"primaryKey": "referenceId"
}
},
{
"dcterms:bibliographicCitation": "Adhurya, Sagar; Lee, Da-Yeong; Park, Young-Seuk (2024). KF-metaweb: A trophic metaweb of freshwater ecosystems of South Korea (Version 1.0) [Dataset]. Dryad. https://doi.org/10.5061/dryad.cz8w9gjbc",
"url": "xlsx:https://datadryad.org/stash/downloads/file_stream/3078242!/Metaweb",
"headerRowCount": 1,
"delimiter": "\t",
"interactionTypeName": "eats",
"interactionTypeId": "http://purl.obolibrary.org/obo/RO_0002470",
"null": [
"NULL",
""
],
"tableSchema": {
"columns": [
{
"name": "targetTaxonId",
"titles": "resource",
"datatype": "string"
},
{
"name": "sourceTaxonId",
"titles": "consumer",
"datatype": "string"
},
{
"name": "referenceId",
"titles": "Reference",
"datatype": "string",
"separator": ","
}
],
"foreignKeys": [
{
"columnReference": "targetTaxonId",
"reference": {
"columnReference": "taxonId"
}
},
{
"columnReference": "sourceTaxonId",
"reference": {
"columnReference": "taxonId"
}
},
{
"columnReference": "referenceId",
"reference": {
"columnReference": "referenceId"
}
}
]
}
},
{
"dcterms:bibliographicCitation": "Adhurya, Sagar; Lee, Da-Yeong; Park, Young-Seuk (2024). KF-metaweb: A trophic metaweb of freshwater ecosystems of South Korea (Version 1.0) [Dataset]. Dryad. https://doi.org/10.5061/dryad.cz8w9gjbc",
"url": "xlsx:https://datadryad.org/stash/downloads/file_stream/3078242!/Node%20Taxonomy",
"headerRowCount": 1,
"delimiter": "\t",
"null": [
"NULL",
""
],
"tableSchema": {
"columns": [
{
"name": "taxonId",
"titles": "Node",
"datatype": "string"
},
{
"name": "taxonGenusName",
"titles": "Genus",
"datatype": "string"
},
{
"name": "taxonFamilyName",
"titles": "Family",
"datatype": "string"
},
{
"name": "taxonOrderName",
"titles": "Order",
"datatype": "string"
},
{
"name": "taxonClassName",
"titles": "Class",
"datatype": "string"
},
{
"name": "taxonPhylumName",
"titles": "Phylum",
"datatype": "string"
},
{
"name": "taxonKingdomName",
"titles": "Kingdom",
"datatype": "string"
},
{
"name": "Category",
"titles": "Category",
"datatype": "string"
}
],
"primaryKey": "taxonId"
}
}
]
}Improvements
- add support for http://purl.obolibrary.org/obo/RO_0008509 [[has roost] , a term introduced by @diatomsRcool
Bug fixes
n/a
Contributors
diatomsRcool
Assets 2
v0.25.19
v0.25.18
Features
n/a
Improvements
- include higher taxa authorities as taxon path shortcut in Taxon Domain object in GloBI core libraries. Related to globalbioticinteractions/name-alignment-template#18 inspired by @whitfarnum
Bug fixes
n/a
Contributors
whitfarnum
Assets 2
v0.25.17
Features
n/a
Improvements
- support occurrenceRemarks with pattern "Collected from ..." see #956
- remove non-breaking whitespaces when parsing lat/lng pairs see #962
- add specific logging for suspicious DwC records https://github.com/BioKIC/Symbiota/issues/758
Bug fixes
n/a
v0.25.16
Features
n/a
Improvements
- reduce memory use when indexing DwC-A; #949
- elton4n - towards clean shutdown of database between running commands to avoid state pollution
Bug fixes
- close DwC-A stream after processing; related to globalbioticinteractions/elton#58
v0.25.15
Features
n/a
Improvements
n/a
Bug fixes
- use tabular info from eml.xml only if a table definition is available in eml globalbioticinteractions/elton#57