Releases | Open Sustainable Technology

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Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen about 1 month ago

Features

Improvements

ignore missing tables for dwc-dp indexing support https://github.com/globalbioticinteractions/globalbioticinteractions/issues/1049 @tucotuco

Bugs

n/a

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen about 1 month ago

Features

initial pass at dwc-dp indexing support https://github.com/globalbioticinteractions/globalbioticinteractions/issues/1049 @tucotuco

Improvements

n/a

Bugs

n/a

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen about 2 months ago

Features

n/a

Improvements

update supported Relations Ontology Mappings; big thanks to @mdrishti @ddooley @cmungall @nataled @bpeters42 @anitacaron for helping to introduce the hasAllelopath, inverse of allelopathOf via oborel/obo-relations#809

Bugs

do not merge table schemas on config override; instead, replace them … …if present

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen about 2 months ago

Features

n/a

Improvements

make hash calculation for cached content configurable (related to https://github.com/globalbioticinteractions/elton/issues/69)

Bugs

n/a

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen about 2 months ago

Features

n/a

Improvements

Bugs

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Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen 2 months ago

Features

n/a

Improvements

improved body part mappings as provided by @mdrishti (thank you!) https://github.com/globalbioticinteractions/globalbioticinteractions/issues/1031 .
towards supporting discoverlife in rendering GloBI search results; re… …lated to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/1038
make default interaction type mappings visible in provenance graphs: make interaction type mappings explicit by shipping them along with the dependency manifest (related to https://github.com/globalbioticinteractions/elton/issues/61)

example

elton update --prov-mode globalbioticinteractions/template-dataset | grep csv | grep hasVersion

results in:

<classpath:/org/globalbioticinteractions/interaction_types_ignored.csv> <http://purl.org/pav/hasVersion> <hash://sha256/f49f665c540214e7d00466e359821de1bc03206f8373d4974220d608ed7b98f3> <urn:uuid:1d66567d-ea58-4b05-b167-42cbf054f5bb> .
<classpath:/org/globalbioticinteractions/interaction_types_mapping.csv> <http://purl.org/pav/hasVersion> <hash://sha256/ef045408607c6fb19d6bdf8145e7ce16a0e16bc8be45acbe31da33e1db0c9ea7> <urn:uuid:1d66567d-ea58-4b05-b167-42cbf054f5bb> .
<classpath:/org/globalbioticinteractions/interaction_types_ro_unmapped.csv> <http://purl.org/pav/hasVersion> <hash://sha256/43aba7b90c686a4890aebd4a90a02d6f82259664524bdad1b22102a29fe9fa07> <urn:uuid:1d66567d-ea58-4b05-b167-42cbf054f5bb> .
<classpath:/org/globalbioticinteractions/interaction_types_ro.csv> <http://purl.org/pav/hasVersion> <hash://sha256/7dc2797003a95ac7b97be06fda48b4dc25e7a555a2839a19ad7dc7a148427e43> <urn:uuid:1d66567d-ea58-4b05-b167-42cbf054f5bb> .

where hash://sha256/ef045408607c6fb19d6bdf8145e7ce16a0e16bc8be45acbe31da33e1db0c9ea7 is the content id/hash of one of the default mappings shipped with Elton -

with

preston cat --remote https://linker.bio hash://sha256/ef045408607c6fb19d6bdf8145e7ce16a0e16bc8be45acbe31da33e1db0c9ea7\
 | head\
 | mlr --icsv --omd cat\
 | head

resulting in:

provided_interaction_type_label	mapped_to_interaction_type_label	mapped_to_interaction_type_id
associated with	interactsWith	http://purl.obolibrary.org/obo/RO_0002437
plant associations	interactsWith	http://purl.obolibrary.org/obo/RO_0002437
	interactsWith	http://purl.obolibrary.org/obo/RO_0002437
ex	hasHost	http://purl.obolibrary.org/obo/RO_0002454
ex.	hasHost	http://purl.obolibrary.org/obo/RO_0002454
reared ex	hasHost	http://purl.obolibrary.org/obo/RO_0002454
reared ex.	hasHost	http://purl.obolibrary.org/obo/RO_0002454
host to	hostOf	http://purl.obolibrary.org/obo/RO_0002453
host	hasHost	http://purl.obolibrary.org/obo/RO_0002454

Bugs

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen 3 months ago

Features

n/a

Improvements

support configuring of specific versions of dataset resources to help work towards behavior described in https://github.com/globalbioticinteractions/globalbioticinteractions/issues/1030 https://github.com/globalbioticinteractions/elton/issues/52 https://github.com/globalbioticinteractions/elton/issues/62

previously,

...
"resources": {
  "https://example.org/old": "https://example.org/new"
}

now,

...
"resources": {
  "https://example.org/old": "https://example.org/new"
},
"versions": {
  "https://example.org/new": "hash://sha256/1234..."
}

which would peg the resource to a specific version (e.g, hash://sha256/1234...)

Bugs

create tmpdir if none exists

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen 4 months ago

Features

n/a

Improvements

CacheUtil improvements to help work towards integration with Preston https://github.com/globalbioticinteractions/globalbioticinteractions/issues/1030 https://github.com/globalbioticinteractions/elton/issues/52

Bugs

n/a

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen 4 months ago

Features

n/a

Improvements

cleanup tmp files on closing of inputstream #999 .

Bugs

n/a

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen 4 months ago

Features

n/a

Improvements

(again) towards separating provenance (i.e. access.tsv) and content (i.e. sha256) paths to facilitate preston-elton interoperability

Bugs

n/a

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen 5 months ago

Features

n/a

Improvements

towards separating provenance (i.e. access.tsv) and content (i.e. sha256) paths

Bugs

n/a

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen 6 months ago

Features

n/a

Improvements

append more aliases for wikipedia; related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/1011
add mapping for allelopathOf for external use
towards separating provenance (i.e. access.tsv) and content (i.e. sha256) paths

Bug fixes

n/a

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen 6 months ago

Features

n/a

Improvements

default workdir to "."
use workdir when tmp files are created https://github.com/globalbioticinteractions/globalbioticinteractions/issues/999
add custom service unavailable strategy as used in https://github.com/bio-guoda/preston/issues/301

Bug fixes

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen 7 months ago

Features

n/a

Improvements

working towards using explicit cache dir to allow for better management of no longer used tmp files https://github.com/globalbioticinteractions/globalbioticinteractions/issues/999

Bug fixes

n/a

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen 9 months ago

Features

n/a

Improvements

Bug fixes

n/a

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen 9 months ago

Features

n/a

Improvements

improve separated values in table cell values; https://github.com/globalbioticinteractions/globalbioticinteractions/issues/982
skip BOM when reading csv/tsv files; related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/992
remove substitution of source doi/urls on reference level to prevent … …sticky study citation seen in https://github.com/globalbioticinteractions/globalbioticinteractions/issues/992
add support for http://purl.obolibrary.org/obo/RO_0002555 (allelopath… … of) related to https://github.com/globalbioticinteractions/globalbioticinteractions/issues/993#issuecomment-2209219735
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 https://github.com/globalbioticinteractions/globalbioticinteractions/issues/997
allow for RO_ prefix in addition to RO: prefixes

Bug fixes

n/a

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen 9 months ago

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

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen 10 months ago

Features

allow for linking of tables via primary/foreign keys in a globi.json schema definition. Inspired by https://github.com/globalbioticinteractions/globalbioticinteractions/issues/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

Biosphere - Biodiversity Data Access and Management - Java
Published by jhpoelen 11 months ago

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