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pmo-base.obo
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format-version: 1.2
data-version: pmo/releases/2021-12-17/pmo-base.owl
remark: Planet Microbe Ontology
ontology: pmo/pmo-base
[Term]
id: PMO:00000000
name: root node
[Term]
id: PMO:00000003
name: unclassified sequences
is_a: NCBITaxon:1
property_value: IAO:0000118 http://purl.obolibrary.org/obo/NCBITaxon_12908 xsd:string
[Term]
id: PMO:00000004
name: metagenomes
is_a: PMO:00000003 ! unclassified sequences
property_value: IAO:0000118 http://purl.obolibrary.org/obo/NCBITaxon_408169 xsd:string
[Term]
id: PMO:00000005
name: site label
def: "A datum lable which serves to lable a site of investigation." []
is_a: IAO:0000009
[Term]
id: PMO:00000006
name: bottle label
is_a: IAO:0000009
property_value: IAO:0000116 "May depricate this term." xsd:string
[Term]
id: PMO:00000007
name: project investigation identifier
def: "An investigation identifier which represents a sampling project." []
is_a: OBI:0001628
property_value: IAO:0000116 "Ex: TARA, OSD, HOT" xsd:string
[Term]
id: PMO:00000008
name: specimen collection time measurement datum start
def: "A time measurement datum that is the measure of the start time when the specimens are collected." []
is_a: OBI:0001619
[Term]
id: PMO:00000009
name: specimen collection time measurement datum stop
def: "A time measurement datum that is the measure of the time when the specimens are finished being collected." []
is_a: OBI:0001619
[Term]
id: PMO:00000010
name: conductivity temperature pressure instrument
def: "A measurement device which measures temperature and pressure." []
is_a: OBI:0000832
[Term]
id: PMO:00000011
name: rosette sampling device
def: "A specimen collection device which is comprised of an assemblage of bottles used to sample water from a water body." [https://en.wikipedia.org/wiki/Rosette_sampler]
is_a: PMO:00000074 ! specimen collection device
[Term]
id: PMO:00000012
name: rosette sampling device niskin position
def: "A part of a rosette sampling device in which a niskin bottle is positioned for deployment." []
is_a: BFO:0000024
property_value: IAO:0000116 "Perhaps depricate this term." xsd:string
[Term]
id: PMO:00000013
name: DEPRECATED salinity
comment: Term Replaced by PATO:0085001
property_value: seeAlso PATO:0085001
is_obsolete: true
[Term]
id: PMO:00000014
name: liquid water salinity
def: "A salinity quality which inheres in liquid water." []
is_a: PATO:0085001
intersection_of: PATO:0085001
intersection_of: RO:0000052 ENVO:00002006
property_value: IAO:0000116 "To add to ENVO." xsd:string
[Term]
id: PMO:00000015
name: photosynthetically active electromagnetic radiation of liquid water
def: "A electromagnetic radiation quality in which photosynthetically active radiation inheres in liquid water." []
intersection_of: PATO:0001291
intersection_of: RO:0000052 ENVO:00002006
property_value: IAO:0000116 "Add to ENVO." xsd:string
[Term]
id: PMO:00000016
name: number of observations averaged to produce device measurment datum
is_a: IAO:0000109
property_value: IAO:0000116 "Perhaps depricate." xsd:string
[Term]
id: PMO:00000017
name: number of observations averaged at pressure level to produce CTD measurment datum
is_a: PMO:00000016 ! number of observations averaged to produce device measurment datum
property_value: IAO:0000116 "Perhaps depricate." xsd:string
[Term]
id: PMO:00000018
name: DEPRECATED concentration of nitrate and nitrite in water
comment: Term replaced by ENVO:03000123
property_value: seeAlso ENVO:03000123
is_obsolete: true
[Term]
id: PMO:00000019
name: replicate
def: "A role played by a biological sample in the context of an experiment where the intent is that biological or technical variation is measured." []
is_a: BFO:0000023
property_value: IAO:0000116 "Find a way to import EFO or use an equivalent class from OBI. Or perhaps depricate." xsd:string
property_value: IAO:0000118 http://www.ebi.ac.uk/efo/EFO_0000683 xsd:string
[Term]
id: PMO:00000020
name: potential temperature
def: "A temperature which would inhere in a bearer if such bearer were adiabatically compressed from it's existing temperature and pressure to a standard presure." [http://paoc.mit.edu/synoptic/courses/12.310/assign3/A3_potential%20temperature.pdf]
comment: Standard pressure is typically one atmosphere.
synonym: "theta" RELATED []
is_a: PATO:0000146
property_value: IAO:0000116 "Add to ENVO or PATO." xsd:string
[Term]
id: PMO:00000021
name: potential density
def: "A density which would inhere in a bearer if such bearer were adiabatically \nbrought to a standard reference pressure." [https://en.wikipedia.org/wiki/Potential_density]
synonym: "sigma" RELATED []
is_a: PATO:0001019
property_value: IAO:0000116 "Add to ENVO or PATO." xsd:string
[Term]
id: PMO:00000022
name: aquatic sample minimum filter fractionation size threshold
def: "A size quality which inheres in an aquatic environmental material sample by virtue of being the minimum particle size obtained when such bearer is subject to a size fractionating filtration process." []
is_a: PMO:00000168 ! aquatic environmental material sample filter fractionation size
property_value: IAO:0000116 "Imporve and add to OBI or BCO." xsd:string
[Term]
id: PMO:00000023
name: aquatic sample maximum filter fractionation size threshold
def: "A size quality which inheres in an aquatic environmental material sample by virtue of being the maximum particle size obtained when such bearer is subject to a size fractionating filtration process." []
is_a: PMO:00000168 ! aquatic environmental material sample filter fractionation size
property_value: IAO:0000116 "Imporve and add to OBI or BCO." xsd:string
[Term]
id: PMO:00000024
name: specimen volume
def: "A volume quality which inheres in a specimen." []
is_a: PATO:0000918
relationship: RO:0000052 OBI:0100051
property_value: IAO:0000116 "Add to OBI or BCO." xsd:string
[Term]
id: PMO:00000025
name: water sample volume
def: "A specimen volume quality which inheres in a specimen which consists of liquid water." []
is_a: PMO:00000024 ! specimen volume
relationship: RO:0000052 ENVO:00002006
property_value: IAO:0000116 "Fix and add to BCO or OBI." xsd:string
[Term]
id: PMO:00000026
name: concentration of chlorophyll in water
is_a: PATO:0000033
property_value: IAO:0000118 http://purl.obolibrary.org/obo/ENVO_3100036 xsd:string
is_obsolete: true
replaced_by: ENVO:3100036
[Term]
id: PMO:00000027
name: concentration of nitrate in water
is_a: PATO:0000033
property_value: IAO:0000118 http://purl.obolibrary.org/obo/ENVO_3100022 xsd:string
is_obsolete: true
replaced_by: ENVO:3100022
[Term]
id: PMO:00000028
name: pressure of water
is_a: PATO:0001025
property_value: IAO:0000118 http://purl.obolibrary.org/obo/ENVO_3100033 xsd:string
is_obsolete: true
replaced_by: ENVO:3100033
[Term]
id: PMO:00000029
name: depth of water
is_a: PATO:0001595
property_value: IAO:0000118 http://purl.obolibrary.org/obo/ENVO_3100031 xsd:string
is_obsolete: true
replaced_by: ENVO:3100031
[Term]
id: PMO:00000030
name: fluorescence of water
is_a: PATO:0000018
property_value: IAO:0000118 http://purl.obolibrary.org/obo/ENVO_3100032 xsd:string
is_obsolete: true
replaced_by: ENVO_3100032
[Term]
id: PMO:00000031
name: concentration of phosphate in water
is_a: PATO:0000033
property_value: IAO:0000118 http://purl.obolibrary.org/obo/ENVO_3100026 xsd:string
is_obsolete: true
replaced_by: ENVO:3100026
[Term]
id: PMO:00000032
name: concentration of silicate(4-) in water
is_a: PATO:0000033
property_value: IAO:0000118 http://purl.obolibrary.org/obo/ENVO_3100027 xsd:string
is_obsolete: true
replaced_by: ENVO:3100027
[Term]
id: PMO:00000033
name: bar
def: "A pressure unit which is equal to 100,000 pascal." [https://en.wikipedia.org/wiki/Bar_(unit)]
is_a: UO:0000109
property_value: IAO:0000116 "Add to UO." xsd:string
[Term]
id: PMO:00000034
name: decibar
def: "A pressure unit which is equal to one tenth of a bar." []
is_a: UO:0000109
property_value: IAO:0000116 "Add to UO." xsd:string
[Term]
id: PMO:00000035
name: atmosphere unit
def: "A pressure unit which is equal to 101325 pascal." [https://en.wikipedia.org/wiki/Atmosphere_(unit)]
is_a: UO:0000109
property_value: IAO:0000116 "Add to UO." xsd:string
[Term]
id: PMO:00000036
name: salinity unit
def: "A unit which is a standard measure of salinity." []
is_a: UO:0000000
property_value: IAO:0000116 "Add to UO." xsd:string
[Term]
id: PMO:00000037
name: practical salinity unit
synonym: "PSS-78" EXACT []
synonym: "PSU" EXACT []
is_a: PMO:00000036 ! salinity unit
property_value: IAO:0000116 "Perhaps don't add to UO. \n\nAccording to http://www.salinityremotesensing.ifremer.fr/sea-surface-salinity/definition-and-units it is equivalent to per thousand." xsd:string
[Term]
id: PMO:00000038
name: international temperature scale of 1990 unit
synonym: "ITS-90" EXACT []
xref: https://www.omega.com/temperature/Z/pdf/z186-193.pdf
is_a: UO:0000005
property_value: IAO:0000116 "Depricate this is not actually a unit, just a scale to convert between Kelvin and Celcius at various pressures." xsd:string
is_obsolete: true
[Term]
id: PMO:00000044
name: Data
property_value: IAO:0000116 "Figure out how to import EDAM." xsd:string
property_value: IAO:0000118 http://edamontology.org/data_0006 xsd:string
[Term]
id: PMO:00000045
name: Identifier
is_a: PMO:00000044 ! Data
property_value: IAO:0000116 "Figure out how to import EDAM." xsd:string
property_value: IAO:0000118 http://edamontology.org/data_0842 xsd:string
[Term]
id: PMO:00000046
name: URI
is_a: PMO:00000045 ! Identifier
property_value: IAO:0000118 http://edamontology.org/data_1047 xsd:string
[Term]
id: PMO:00000047
name: URL
is_a: PMO:00000046 ! URI
property_value: IAO:0000118 http://edamontology.org/data_1052 xsd:string
[Term]
id: PMO:00000048
name: data submission date
def: "A data item that is the date in which a data item was submitted to a central registry." []
is_a: IAO:0000027
property_value: IAO:0000116 "Clean and add to IAO." xsd:string
[Term]
id: PMO:00000049
name: data submission update date
def: "A data item that is the date in which a data item previously submitted to a central registry was updated." []
is_a: PMO:00000048 ! data submission date
property_value: IAO:0000116 "Add to IAO." xsd:string
[Term]
id: PMO:00000050
name: number of specimen collection devices employed
is_a: IAO:0000109
equivalent_to: PMO:00000051 ! number of niskin bottles deployed during speciment collection process event
property_value: IAO:0000116 "consider for deprication." xsd:string
[Term]
id: PMO:00000051
name: number of niskin bottles deployed during speciment collection process event
property_value: IAO:0000116 "Consider for deprication." xsd:string
[Term]
id: PMO:00000052
name: maximum depth of water collected during specimen collection process
def: "A depth of water quality which inheres in a bearer by virtue of such bearer being the maximum depth of water collected during a specimen collection process." []
is_a: ENVO:3100031
property_value: IAO:0000116 "Perhaps this term should be pushed to BCO or OBI? Or handled with two semantics a maximum quality and ENVO: depth of water." xsd:string
[Term]
id: PMO:00000053
name: maximum pressure of water collected during specimen collection process
def: "A pressure of water quality which inheres in a bearer by virtue of such bearer being the maximum pressure of water collected during a specimen collection process." []
is_a: ENVO:3100033
property_value: IAO:0000116 "Perhaps this term should be pushed to BCO or OBI? Or handled with two semantics a maximum quality and ENVO: pressure of water." xsd:string
[Term]
id: PMO:00000054
name: number designating study site
is_a: IAO:0000109
property_value: IAO:0000116 "Perhaps this term should be pushed to BCO or OBI?" xsd:string
[Term]
id: PMO:00000056
name: centrally registered specimen collection event identifier
def: "A centrally registered event identifier which designates a specimen collection process event." []
is_a: IAO:0000578
property_value: IAO:0000116 "Perhaps this term should be pushed to BCO or OBI?\n\nAdd axiom linking to specimen collection process http://purl.obolibrary.org/obo/OBI_0000659" xsd:string
[Term]
id: PMO:00000057
name: ctd cast number
is_a: PMO:00000056 ! centrally registered specimen collection event identifier
property_value: IAO:0000116 "Perhaps useful perhaps consider for deprication?" xsd:string
[Term]
id: PMO:00000058
name: sampling expedition
is_a: OBI:0000011
property_value: IAO:0000116 "sampling campaign, perhaps useful perhaps depricate." xsd:string
[Term]
id: PMO:00000059
name: sampling expedition leg
is_a: PMO:00000058 ! sampling expedition
property_value: IAO:0000116 "Perhaps consider for deprication." xsd:string
[Term]
id: PMO:00000060
name: sampling expedition identifier
def: "An investigation identifier which represents a sampling expedition campaign." []
is_a: OBI:0001628
property_value: IAO:0000116 "sampling campaign Ex: TARA ocean, Tara arctic OSD 2014, HOT194 etc. Perhaps push to BCO?" xsd:string
[Term]
id: PMO:00000061
name: Name
is_a: PMO:00000045 ! Identifier
property_value: IAO:0000118 http://edamontology.org/data_2099 xsd:string
[Term]
id: PMO:00000062
name: File Name
is_a: PMO:00000061 ! Name
property_value: IAO:0000118 http://edamontology.org/data_1050 xsd:string
[Term]
id: PMO:00000063
name: Summary File Name
is_a: PMO:00000062 ! File Name
[Term]
id: PMO:00000065
name: sampling expedition project investigation and leg identifier
is_a: PMO:00000060 ! sampling expedition identifier
property_value: IAO:0000116 "Consider for deprication." xsd:string
[Term]
id: PMO:00000066
name: repeated expedition location identifier
is_a: PMO:00000060 ! sampling expedition identifier
property_value: IAO:0000116 "Perhaps consider for deprication. Maybe same as superclass samplping expedition identifier." xsd:string
[Term]
id: PMO:00000067
name: navigation device
is_a: OBI:0000968
property_value: IAO:0000116 "Perhaps consider for deprication." xsd:string
[Term]
id: PMO:00000068
name: global positioning system device
is_a: PMO:00000067 ! navigation device
property_value: IAO:0000116 "Perhaps consider for deprication." xsd:string
[Term]
id: PMO:00000069
name: genomic library preparation device
def: "A device which is used to prepare a genomic library." []
is_a: OBI:0000968
property_value: IAO:0000116 "Could be useful semantic to push to OBI." xsd:string
[Term]
id: PMO:00000070
name: data publication date
def: "A data item which indicates the publication date of a dataset." []
is_a: IAO:0000027
property_value: IAO:0000116 "Perhaps could make more general just \"publication date\" and not have it be specific to a dataset." xsd:string
[Term]
id: PMO:00000071
name: length of DNA sequence data
def: "A length which inheres in a DNA sequence datum namely the number of basepairs in the sequence." []
is_a: PATO:0000122
property_value: IAO:0000116 "Perhaps useful semantic to push to OBI?" xsd:string
[Term]
id: PMO:00000072
name: file size
is_a: PATO:0000117
[Term]
id: PMO:00000073
name: number of locations sequenced within a DNA sequence
def: "A measurment datum which describes the number of locations sequenced witin a DNA sequence." []
is_a: IAO:0000109
property_value: IAO:0000116 "Unsure if this is worth pushing to IAO or BCO." xsd:string
[Term]
id: PMO:00000074
name: specimen collection device
def: "A device which is used to collect a specimen during a specimen collection process." []
is_a: OBI:0000968
property_value: IAO:0000116 "Definately should push to OBI or BCO." xsd:string
[Term]
id: PMO:00000075
name: comment on investigation
def: "A textual entity that is about any of the aspects of an investigation worth noting." []
is_a: IAO:0000300
property_value: IAO:0000116 "Reimport the OBI term after the axiom has been fixed, as it's currently failing when run with the ELK reasoner." xsd:string
property_value: IAO:0000118 http://purl.obolibrary.org/obo/OBI_0001898 xsd:string
[Term]
id: PMO:00000076
name: latitude coordinate measurement datum start
def: "A measurement datum that is the measure of the starting latitude coordinate of a site during a specimen collection process." []
is_a: OBI:0001620
property_value: IAO:0000116 "Add to BCO." xsd:string
[Term]
id: PMO:00000077
name: longitude coordinate measurement datum start
def: "A measurement datum that is the measure of the starting longitude coordinate of a site during a specimen collection process." []
is_a: OBI:0001621
property_value: IAO:0000116 "Add to BCO." xsd:string
[Term]
id: PMO:00000078
name: longitude coordinate measurement datum stop
def: "A measurement datum that is the measure of the longitude coordinate of a site at the end of a specimen collection process." []
is_a: OBI:0001621
property_value: IAO:0000116 "Add to BCO." xsd:string
[Term]
id: PMO:00000079
name: latitude coordinate measurement datum stop
def: "A measurement datum that is the measure of the latitude coordinate of a site at the end of a specimen collection process." []
is_a: OBI:0001620
property_value: IAO:0000116 "Add to BCO." xsd:string
[Term]
id: PMO:00000080
name: time zone
is_a: IAO:0000416
property_value: IAO:0000116 "e.g. UTC+00 from OSD. Consider for deprication." xsd:string
[Term]
id: PMO:00000081
name: specimen collection time measurement datum in localized time zone
def: "A specimen collection time measurement datum which is measured in a localized time zone." []
is_a: OBI:0001619
property_value: IAO:0000116 "Don't depricate, could be a useful semantic for future systems, check with Ramona Walls" xsd:string
[Term]
id: PMO:00000083
name: distance between site and country border
def: "A distance which seperates a site from the nearest boarder of a country." []
is_a: PATO:0000040
property_value: IAO:0000116 "Add to BCO or depricate." xsd:string
[Term]
id: PMO:00000084
name: geographic region
is_a: BFO:0000009
property_value: IAO:0000116 "Perhaps in the future the 'geographic location' hierarchy from GAZ should be rooted there? Check where this term is being used and perhaps deprecate if un-needed." xsd:string
[Term]
id: PMO:00000085
name: biogeochemical province
def: "A geographic location which represents a division of the world oceans into provinces as defined by Longhurst (1995; 1998; 2006)." []
synonym: "Longhurst Province" EXACT []
xref: http://marineregions.org/sources.php
is_a: PMO:00000088 ! geographic location
property_value: IAO:0000116 "Perhaps add to ENVO or GAZ. Depending on status of integration of marineregions.org into GAZ. See https://github.com/EnvironmentOntology/gaz/issues/29" xsd:string
property_value: IAO:0000118 http://marineregions.org/gazetteer.php?p=details&id=22538 xsd:string
[Term]
id: PMO:00000086
name: biogeochemical province label
is_a: IAO:0000009
property_value: IAO:0000116 "link to biogeochemical province. Consider for deprecation." xsd:string
[Term]
id: PMO:00000087
name: distance between site and biogeochemical province
is_a: PATO:0000040
property_value: IAO:0000116 "Add to BCO or depricate." xsd:string
[Term]
id: PMO:00000088
name: geographic location
property_value: IAO:0000116 "perhaps this could be subclass to 'two-dimensional spatial region' http://purl.obolibrary.org/obo/BFO_0000009" xsd:string
property_value: IAO:0000118 http://purl.obolibrary.org/obo/GAZ_00000448 xsd:string
[Term]
id: PMO:00000089
name: Oceans and Seas
is_a: PMO:00000088 ! geographic location
property_value: IAO:0000116 "Figure out how to import from GAZ." xsd:string
property_value: IAO:0000118 http://purl.obolibrary.org/obo/GAZ_00000590 xsd:string
[Term]
id: PMO:00000090
name: distance between a site and a geographic location
is_a: PATO:0000040
property_value: IAO:0000116 "add link to http://purl.obolibrary.org/obo/GAZ_00000448" xsd:string
property_value: IAO:0000116 "Add to BCO or depricate." xsd:string
[Term]
id: PMO:00000091
name: Large Marine Ecosystem
def: "A geograpphic location which comprises a natural region of ocean space encompassing coastal waters from river basins and estuaries to the seaward boundary of continental shelves and the outer margins of coastal currents." []
xref: http://marineregions.org/sources.php
is_a: PMO:00000088 ! geographic location
property_value: IAO:0000116 "Perhaps in the future we could map or at least create GAZ classes for the top levels the Marineregions.org gazetteer." xsd:string
property_value: IAO:0000118 http://marineregions.org/gazetteer.php?p=details&id=22539 xsd:string
[Term]
id: PMO:00000092
name: International Hydrographic Organization Sea Area
def: "A geographic location which has been registered in the International Hydrographic Organization Sea Area database." []
xref: http://marineregions.org/sources.php
is_a: PMO:00000088 ! geographic location
property_value: IAO:0000116 "From http://www.marineregions.org/sources.php. Figure out how to integrate with GAZ and or ENVO." xsd:string
[Term]
id: PMO:00000093
name: specimen collection process data doccument
def: "A doccument which comprises raw data collected during a specimen collection process." []
is_a: IAO:0000310
property_value: IAO:0000116 "Add to BCO." xsd:string
property_value: IAO:0000116 "Original sampling handbook or checklist from a sampling experiment or specimen collection process." xsd:string
[Term]
id: PMO:00000100
name: plankton aggregate
def: "A multi-species collection of planktonic organisms which have been aggregrated as a result of a specimen collection process." []
is_a: PCO:0000029
property_value: IAO:0000116 "Clean and add to PCO or BCO." xsd:string
[Term]
id: PMO:00000101
name: nanoplankton and microplankton aggregate
def: "A plankton aggregate which comprises aggregated nanoplankton and microplankton." []
is_a: PMO:00000100 ! plankton aggregate
property_value: IAO:0000116 "add axioms to link to http://purl.obolibrary.org/obo/PMO_00000106 and http://purl.obolibrary.org/obo/PMO_00000105" xsd:string
[Term]
id: PMO:00000102
name: dissolved organic carbon
def: "An aggregate of organic carbon-containing molecules derived from an environmental material which pass through a filter during a specimen collection process." [] {http://purl.obolibrary.org/obo/IAO_0000119="https://en.wikipedia.org/wiki/Total_organic_carbon"}
is_a: PMO:00000109 ! aggregation of carbon molecules
property_value: IAO:0000116 "Clean and add to ENVO." xsd:string
[Term]
id: PMO:00000103
name: particulate organic carbon
def: "An aggregate of organic carbon-containing molecules derived from an environmental material which are too large to pass through a filter during a specimen collection process." [] {http://purl.obolibrary.org/obo/IAO_0000119="https://en.wikipedia.org/wiki/Total_organic_carbon"}
synonym: "suspended organic carbon" EXACT []
is_a: PMO:00000109 ! aggregation of carbon molecules
property_value: IAO:0000116 "Clean and add to ENVO." xsd:string
[Term]
id: PMO:00000105
name: microplankton material
def: "A portion of planktonic material which is comprised of plankton which range in size between 20 and 200 micrometers." [https://en.wikipedia.org/wiki/Plankton#Size_groups]
synonym: "Microplankton" NARROW []
is_a: ENVO:01000063
property_value: IAO:0000116 "Add to ENVO." xsd:string
[Term]
id: PMO:00000106
name: nanophytoplankton material
def: "A portion of planktonic material which is comprised of plankton which range in size between 2 and 20 micrometers." [https://en.wikipedia.org/wiki/Plankton#Size_groups]
synonym: "Nanoplankton" NARROW []
is_a: ENVO:01000063
property_value: IAO:0000116 "Add to ENVO." xsd:string
property_value: IAO:0000119 https://en.wikipedia.org/wiki/Plankton#Size_groups xsd:string
[Term]
id: PMO:00000107
name: autotrophic biomass formation process
def: "A process during which an organism produces biomass from abiotic components using an autotrophic growth process." []
synonym: "primary productivity" BROAD []
is_a: PMO:00000117 ! biomass formation process
property_value: IAO:0000116 "link to PMO_00000108, and add to ENVO." xsd:string
[Term]
id: PMO:00000108
name: primary productivity carbon
def: "An aggregation of carbon molecules which constitute biomass accumulated during an autotrophic biomass formation process." []
is_a: PMO:00000109 ! aggregation of carbon molecules
property_value: IAO:0000116 "link to http://purl.obolibrary.org/obo/PMO_00000107, clean and add to ENVO." xsd:string
[Term]
id: PMO:00000109
name: aggregation of carbon molecules
def: "An object aggregate which is composed primarily of carbon molecules." []
is_a: BFO:0000027
property_value: IAO:0000116 "Link to CHEBI carbon molecule" xsd:string
[Term]
id: PMO:00000110
name: aggregation of nitrogen molecules
def: "An object aggregate which is composed primarily of nitrogen molecules." []
is_a: BFO:0000027
property_value: IAO:0000116 "Clean and add to ENVO." xsd:string
property_value: IAO:0000116 "Link to CHEBI nitrogen molecule." xsd:string
[Term]
id: PMO:00000111
name: dissolved organic nitrogen
def: "An aggregate of nitrogen and carbon-containing molecules derived from an environmental material which pass through a filter during a specimen collection process." [https://www.sciencedirect.com/topics/earth-and-planetary-sciences/dissolved-organic-nitrogen]
is_a: PMO:00000110 ! aggregation of nitrogen molecules
property_value: IAO:0000116 "Add to ENVO." xsd:string
[Term]
id: PMO:00000112
name: particulate organic nitrogen
def: "An aggregate of organic nitrogen and carbon-containing molecules derived from an environmental material which are too large to pass through a filter during a specimen collection process." [https://www.sciencedirect.com/topics/earth-and-planetary-sciences/particulate-organic-nitrogen]
is_a: PMO:00000110 ! aggregation of nitrogen molecules
property_value: IAO:0000116 "Add to ENVO." xsd:string
[Term]
id: PMO:00000113
name: mesoplankton material
def: "A portion of planktonic material which is comprised of plankton which range in size between 0.2 and 20 milimeters." [https://en.wikipedia.org/wiki/Plankton#Size_groups]
synonym: "Mesoplankton" NARROW []
is_a: ENVO:01000063
property_value: IAO:0000116 "Add to ENVO." xsd:string
[Term]
id: PMO:00000114
name: mesoplankton and macroplankton aggregate
def: "A plankton aggregate which comprises aggregated mesoplankton and macroplankton." []
is_a: PMO:00000100 ! plankton aggregate
property_value: IAO:0000116 "Add to ENVO." xsd:string
property_value: IAO:0000116 "link to http://purl.obolibrary.org/obo/PMO_00000115 and http://purl.obolibrary.org/obo/PMO_00000113" xsd:string
[Term]
id: PMO:00000115
name: macroplankton material
def: "A portion of planktonic material which is comprised of plankton which range in size between 2 and 20 centimeters." [https://en.wikipedia.org/wiki/Plankton#Size_groups]
synonym: "Macroplankton" NARROW []
is_a: ENVO:01000063
property_value: IAO:0000116 "Add to ENVO." xsd:string
[Term]
id: PMO:00000116
name: prokaryote derived carbon
def: "An aggregate of carbon-containing molecules which were derived from a prokaryotic biomass formation process." []
is_a: PMO:00000109 ! aggregation of carbon molecules
property_value: IAO:0000116 "Add to ENVO." xsd:string
[Term]
id: PMO:00000117
name: biomass formation process
def: "An environmental system process during which growing organsims produce new biomass." []
is_a: ENVO:02500000
property_value: IAO:0000116 "Clean definition, add axioms and add to ENVO." xsd:string
[Term]
id: PMO:00000118
name: prokaryotic biomass formation process
def: "A biomass formation process during which prokaryotic organisms create novel biomass." []
is_a: PMO:00000117 ! biomass formation process
property_value: IAO:0000116 "Clean definition, add axioms and add to ENVO." xsd:string
[Term]
id: PMO:00000120
name: turbidity
def: "A physical quality which inheres in a fluid bearer by virtue of the bearer being cloudy or hazy due to a large numbers of individual particles within such bearer." [https://en.wikipedia.org/wiki/Turbidity, https://www.isanorcal.org/download/tech2007_presentations/turbidity.pdf]
is_a: PATO:0001018
property_value: IAO:0000116 "Add to PATO." xsd:string
[Term]
id: PMO:00000121
name: turbidity of water
def: "A turbidity quality which inheres in a water bearer." []
is_a: PMO:00000120 ! turbidity
property_value: IAO:0000116 "Add to ENVO or PATO." xsd:string
[Term]
id: PMO:00000122
name: Biosample identifier assigned by the National Center for Biotechnology Information
def: "A specimen identifier assigned by sequencing facility which is assigned by the National Center for Biotechnology Information." []
is_a: OBI:0001901
property_value: IAO:0000116 "example SAMEA3275646 https://www.ncbi.nlm.nih.gov/biosample/?term=SAMEA3275646. I wonder if this should perhaps be an instance of a specimen identifier assigned by sequencing facility class rather then a subclass of it.\n\nUse the OBI superclass as primary key for PM, condsider this class for deprication." xsd:string
[Term]
id: PMO:00000123
name: SRA accession number
def: "A specimen identifier assigned by sequencing facility which identifies a Sequence Read Archive (SRA) acession number." []
synonym: "Secondary sample accession" EXACT []
is_a: OBI:0001901
property_value: IAO:0000116 "example ERS667668 https://www.ebi.ac.uk/ena/data/view/ERS667668" xsd:string
[Term]
id: PMO:00000124
name: INSDC bioarchive accession number
def: "A specimen identifier assigned by sequencing facility which identifies an International Nucleotide Sequence Database Collaboration (INSDC) bioarchive accession number." []
is_a: OBI:0001901
property_value: IAO:0000116 "Perhaps OSD accession numbers (which this represents) are for DDBJ\nsee https://www.ncbi.nlm.nih.gov/Sequin/acc.html where the prefix AB is a code for a DDBJ direction submission. Consider for deprecation?" xsd:string
[Term]
id: PMO:00000125
name: material flux unit
def: "A unit which is a measure of flux which is typically expressed as volume per area per unit of time." []
is_a: UO:0000000
property_value: IAO:0000116 "Add to UO." xsd:string
property_value: IAO:0000116 "similar to the example from http://reverseosmosischemicals.com/reverse-osmosis-guides/reverse-osmosis-glossary-terms/flux-water-flux-reverse-osmosis-systems" xsd:string
[Term]
id: PMO:00000126
name: micromole per square meter per second
def: "A material flux unit which is equal to one micromole per square meter per second." []
is_a: PMO:00000125 ! material flux unit
property_value: IAO:0000116 "Add to UO." xsd:string
[Term]
id: PMO:00000127
name: mass density rate unit
def: "A mass density unit which proccedes over time." []
is_a: UO:0000000
[Term]
id: PMO:00000128
name: miligram per cubic meter per day
def: "A mass density rate unit which is equal to one miligram per cubic meter per day." []
is_a: PMO:00000127 ! mass density rate unit
property_value: IAO:0000116 "Add to UO." xsd:string
[Term]
id: PMO:00000129
name: unit per cubic meter
def: "A unit per milliliter unit which is equal to one unit of an agreed arbitrary amount per one cubic meter." []
is_a: UO:0000177
property_value: IAO:0000116 "Add to UO." xsd:string
[Term]
id: PMO:00000130
name: milisiemens per centimeter
def: "An electrical conduction unit which is equal to one milisiemen per centimeter." []
is_a: UO:0000262
property_value: IAO:0000116 "Add to UO." xsd:string
[Term]
id: PMO:00000131
name: formazin turbidity unit
def: "A turbidity unit in which a suspension of 1.25 mg/L hydrazine sulfate and 12.5 mg/L hexamethylenetetramine in liquid water has a turbidity of one." [https://en.wikipedia.org/wiki/Formazine]
is_a: UO:0000315
property_value: IAO:0000116 "Clean and add to UO." xsd:string
[Term]
id: PMO:00000132
name: miligram per cubic meter
is_a: UO:0000052
property_value: http://purl.org/dc/elements/1.1/description "A mass unit density which is equal to mass of an object in miligrams divided by the volume in cubic meters." xsd:string
property_value: IAO:0000116 "Add to UO." xsd:string
[Term]
id: PMO:00000133
name: project url
is_a: PMO:00000047 ! URL
property_value: IAO:0000116 "Consider for deprecation." xsd:string
property_value: IAO:0000116 "links to the same idea of a project as 'project investigation identifier'" xsd:string
[Term]
id: PMO:00000134
name: centrally registered identifier url
is_a: PMO:00000047 ! URL
property_value: IAO:0000116 "a link to a centrally registered identifier. Consider for deprecation." xsd:string
[Term]
id: PMO:00000136
name: sampling expedition time measurement datum
def: "A time measurement datum that is the measure of the time when a sampling expedition is conducted." []
is_a: IAO:0000416
property_value: IAO:0000116 "Perhaps add to BCO." xsd:string
[Term]
id: PMO:00000137
name: sampling expedition time measurement datum start
def: "A time measurement datum that is the measure of the starting time when a sampling expedition is conducted." []
is_a: PMO:00000136 ! sampling expedition time measurement datum
property_value: IAO:0000116 "Perhaps add to BCO." xsd:string
[Term]
id: PMO:00000138
name: sampling expedition time measurement datum stop
def: "A time measurement datum that is the measure of the time when a sampling expedition is concluded." []
is_a: PMO:00000136 ! sampling expedition time measurement datum
property_value: IAO:0000116 "Perhaps add to BCO." xsd:string
[Term]
id: PMO:00000139
name: alkalinity of water
def: "The alkalinity of some liquid water." []
is_a: PATO:0001430
property_value: IAO:0000116 "Add to ENVO or PATO." xsd:string
[Term]
id: PMO:00000140
name: equivalent unit
def: "A unit which represents a standard measurment of the amount of a substance that reacts with an arbitrary amount of another substance in a given chemical reaction." [https://en.wikipedia.org/wiki/Equivalent_(chemistry)]
is_a: UO:0000000
property_value: IAO:0000116 "Add to UO." xsd:string
[Term]
id: PMO:00000141
name: microequivalent per kilogram
def: "An equivalent unit which is equal to one microequivalent per kilogram." []
is_a: PMO:00000140 ! equivalent unit
property_value: IAO:0000116 "Add to UO." xsd:string
[Term]
id: PMO:00000142
name: dissolved inorganic carbon
def: "An aggregation of carbon molecules which comprises the sum of inorganic carbon species in a solution including carbon dioxide, carbonic acid, bicarbonate anion, and carbonate." [https://en.wikipedia.org/wiki/Total_inorganic_carbon]
synonym: "total inorganic carbon" EXACT []
is_a: PMO:00000109 ! aggregation of carbon molecules
property_value: IAO:0000116 "Add to ENVO." xsd:string
property_value: IAO:0000116 "CT = [CO2*] + [HCO3−] + [CO32−]" xsd:string
[Term]
id: PMO:00000143
name: sampling expedition site
def: "A site in which a sampling expidition process occurs." []
is_a: BFO:0000029
property_value: IAO:0000116 "Clean maybe change to specimen collection instead of sampling expedition? Add axiom and add to BCO." xsd:string
[Term]
id: PMO:00000144
name: sampling expedition start location
def: "A site in which a sampling expidition process begins." []
is_a: PMO:00000143 ! sampling expedition site
property_value: IAO:0000116 "Clean maybe change to specimen collection instead of sampling expedition? Add axiom and add to BCO." xsd:string
[Term]
id: PMO:00000145
name: sampling expedition end location
def: "A site in which a sampling expidition process terminates." []
is_a: PMO:00000143 ! sampling expedition site
property_value: IAO:0000116 "Clean maybe change to specimen collection instead of sampling expedition? Add axiom and add to BCO." xsd:string
[Term]
id: PMO:00000146
name: conductivity temperature pressure sampling process
def: "A material sampling process during which a conductivity temperature and pressure sampling device is employed." []
is_a: OBI:0000744
property_value: IAO:0000116 "Clean maybe change to specimen collection instead of sampling collection? Add axiom and add to BCO." xsd:string
property_value: IAO:0000116 "Should be observing process" xsd:string
property_value: IAO:0000116 "To conduct a material sampling process using a CTD to gather information about the water column. May need another subclass between this and material sampling process." xsd:string
[Term]
id: PMO:00000147
name: net tow sampling process
def: "A material sampling process during which a net is towed through an aquatic water body in order to collect a sample of organisms residing there in." []
is_a: OBI:0000744
property_value: IAO:0000116 "Clean and add axiom and add to BCO. Ramona wants this." xsd:string
[Term]
id: PMO:00000148
name: remote observation sampling process
def: "A material sampling process during which observations and measurments are taken by a remote measrument device which is not in physical contact with the site under observation." []
comment: For example a satellite measurement.
is_a: OBI:0000744
property_value: IAO:0000116 "Clean and add axiom and add to BCO." xsd:string
[Term]
id: PMO:00000149
name: specimen collection process site
def: "A site where a specimen collection process occurs." []
is_a: BFO:0000029
property_value: IAO:0000116 "Clean and add to BCO." xsd:string
[Term]
id: PMO:00000150
name: particulate carbon
def: "An aggregation of carbon-containing molecules derived from an environmental material which are too large to pass through a filter during a specimen collection process." [http://hahana.soest.hawaii.edu/hot/protocols/protocols.html#]
is_a: PMO:00000109 ! aggregation of carbon molecules
property_value: IAO:0000116 "Add to ENVO." xsd:string
[Term]
id: PMO:00000151
name: particulate nitrogen
def: "An aggregation of nitrogen-containing molecules derived from an environmental material which are too large to pass through a filter during a specimen collection process." [http://hahana.soest.hawaii.edu/hot/protocols/protocols.html#]
is_a: PMO:00000110 ! aggregation of nitrogen molecules
property_value: IAO:0000116 "Add to ENVO." xsd:string
[Term]
id: PMO:00000152
name: aggregation of phosphorus molecules
def: "An object aggregate which is composed primarily of phosphorus molecules." []
is_a: BFO:0000027
property_value: IAO:0000116 "Link to CHEBI clean and add to ENVO." xsd:string
[Term]
id: PMO:00000153
name: particulate phosphorus
def: "An aggregate of phosphorus-containing molecules derived from an environmental material which are too large to pass through a filter during a specimen collection process." [http://hahana.soest.hawaii.edu/hot/protocols/protocols.html#]
is_a: PMO:00000152 ! aggregation of phosphorus molecules
property_value: IAO:0000116 "Add to ENVO." xsd:string
[Term]
id: PMO:00000154
name: nanomole per kilogram
def: "A specific concentration unit which is equal to 1 nanomole of a given substance per kilogram of solvent." []
is_a: UO:0000067
property_value: IAO:0000116 "Add to UO." xsd:string
[Term]
id: PMO:00000155
name: nanogram per liter
def: "A mass unit density which is equal to mass of an object in nanograms divided by the volume in liters." []
is_a: UO:0000052
property_value: IAO:0000116 "Add to UO." xsd:string
[Term]
id: PMO:00000156
name: concentration of 19'-butanoyloxyfucoxanthin in liquid water
def: "The concentration of 19'-butanoyloxyfucoxanthin when measured in liquid water." [https://epic.awi.de/id/eprint/28819/]
is_a: PATO:0000033
property_value: IAO:0000116 "Need to request 19'-butanoyloxyfucoxanthin in CHEBI, then can add to ENVO." xsd:string
[Term]
id: PMO:00000157
name: concentration of 19'-hexanoyloxyfucoxanthin in liquid water
def: "The concentration of 19'-hexanoyloxyfucoxanthin when measured in liquid water." [https://pubchem.ncbi.nlm.nih.gov/compound/6443044]
is_a: PATO:0000033
property_value: IAO:0000116 "Need to request 19'-hexanoyloxyfucoxanthin in CHEBI, then can add to ENVO." xsd:string
[Term]
id: PMO:00000158
name: measure relating to enumeration of aggregation of organisms
def: "A measure, which refers to an aggregation of organisms." []
is_a: IAO:0000109
property_value: IAO:0000116 "Add axiom for organisms, and push to PATO or ECOCORE." xsd:string
property_value: IAO:0000116 "Pattern similar to http://purl.obolibrary.org/obo/IDOMAL_0000428" xsd:string
[Term]
id: PMO:00000159
name: enumeration of Prochlorococcus aggregation
def: "A measure which describes the enumeration of aggregated Prochlorococcus." []
is_a: PMO:00000158 ! measure relating to enumeration of aggregation of organisms
property_value: IAO:0000116 "Add axiom for Procholorococcus, and push to PATO or ECOCORE." xsd:string
[Term]
id: PMO:00000160
name: enumeration of Synechococcus aggregation