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Genomic Biodiversity Interest Group
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DwC Mapping - MIXS:0000010 geo_loc_name #16

Closed tucotuco closed 3 years ago

tucotuco commented 3 years ago
Field Value
subject_id http://rs.tdwg.org/dwc/terms/higherGeography
subject_definition A list (concatenated and separated) of geographic names less specific than the information captured in the locality term.
subject_usage_notes Recommended best practice is to separate the values in a list with space vertical bar space ( | ), with terms in order from least specific to most specific.
subject_examples North Atlantic Ocean, "South America | Argentina | Patagonia | Parque Nacional Nahuel Huapi | Neuquén | Los Lagos" (with accompanying values South America in continent, Argentina in country, Neuquén in stateProvince, and Los Lagos in county.
predicate_id skos:exactMatch
object_id MIXS:0000010
object_label geo_loc_name
object definition The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ)
object source https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
comment DwC term encompasses any combination of geographic region names, while the MIxS term may either be the name of a country or a sea, followed by additional region information.
ymgan commented 3 years ago

Related issues for MIxS v6:

raissameyer commented 3 years ago

Additional Mapping option:

Field Value
subject_id http://rs.tdwg.org/dwc/terms/country
subject_definition The name of the country or major administrative unit in which the Location occurs.
subject_usage_notes Recommended best practice is to use a controlled vocabulary such as the Getty Thesaurus of Geographic Names.
subject_value_syntax - expected_value - unit {term}
subject_examples Denmark, Colombia, España
predicate_id skos:broadMatch
syntax_predicate_id skos:relatedMatch
object_id MIXS:0000010
object_label geo_loc_name
object definition The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ)
object_value_syntax - expected_value - unit country or sea name (INSDC or GAZ);region(GAZ);specific location name - {term};{term};{text}
object source https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
comment the MIxS term includes both seas and countries, while DwC only refers to the country.
syntax_comment The DwC example only expects one word, while MIxS expects two words (country or sea name + specific region name). Additionally MIxS expects terms from an ontology where appropriate, for which the input would not only be a word but a termLabel[termID] combination
raissameyer commented 3 years ago

Suggested syntax predicate for the mapping above https://github.com/tdwg/gbwg/issues/16#issue-805160075

Field Value
subject_id http://rs.tdwg.org/dwc/terms/higherGeography
subject_value_syntax - expected_value - unit {term} | {term} | ... - geographic names
syntax_predicate_id skos:relatedMatch
object_id MIXS:0000010
object_value_syntax - expected_value - unit {term};{term};{text} - country or sea name (INSDC or GAZ);region(GAZ);specific location name
syntax_comment DwC expects a list (of undefined length) of values separated by a vertical bar space " ", while MIxS expects two words (country or sea name + specific region name). Additionally MIxS expects terms from an ontology where appropriate, for which the input would not only be a word but a termLabel[termID] combination
timrobertson100 commented 3 years ago

Perhaps dwc:waterBody may be relevant here

tucotuco commented 3 years ago

Yes, it should be. Country and waterbody are disjunct concepts in Darwin Core.

On Tue, May 11, 2021 at 12:18 PM Tim Robertson @.***> wrote:

Perhaps dwc:waterBody https://dwc.tdwg.org/list/#dwc_waterBody may be relevant here

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/tdwg/gbwg/issues/16#issuecomment-838663894, or unsubscribe https://github.com/notifications/unsubscribe-auth/AADQ72YWXKHNXWIGQQKCME3TNFDDJANCNFSM4XMHXXGQ .

raissameyer commented 3 years ago

Additional Mapping option raised above:

Field Value
subject_id http://rs.tdwg.org/dwc/terms/waterBody
subject_definition The name of the water body in which the Location occurs.
subject_usage_notes Recommended best practice is to use a controlled vocabulary such as the Getty Thesaurus of Geographic Names.
subject_value_syntax - expected_value - unit {term}
subject_examples Indian Ocean, Baltic Sea, Hudson River, Lago Nahuel Huapi
predicate_id skos:broadMatch
syntax_predicate_id skos:relatedMatch
object_id MIXS:0000010
object_label geo_loc_name
object definition The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ)
object_value_syntax - expected_value - unit country or sea name (INSDC or GAZ);region(GAZ);specific location name - {term};{term};{text}
object source https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
comment the MIxS term includes both seas and countries, while DwC only refers to the sea.
syntax_comment The DwC example only expects one sea identifier, while MIxS expects an additional word (country or sea name + specific region name). Additionally, MIxS expects terms from an ontology where appropriate, for which the input would not only be a word but a termLabel[termID] combination