ࡱ> LNK_ 0bjbj 7L5\5\( dddddxxxx<4x v$8">ddd???dd????PyAz{'?w0 ?v"?v"??v"dS$?? v" > *: uc-52-query-4-9-10-onto-additions April 17, 2015 Chase LeCroy last updated: 2015-04-20 Semantic concepts needed in ontology for each query from UC 52. Those still needed in bold; those already completed and approved in WebProtege in grey. Q4: areal CO2 uptake rate by natural phytoplankton communities 1. Carbon cycle components 1.1. Carbon flux 1.1.1. Primary production carbon flux 1.1.1.1. Net primary production carbon flux 1.1.1.1.1. Annual net primary productivity (timescale or rate is not specific) 1.2. Carbon dioxide Carbon dioxide - IRI: HYPERLINK "http://purl.obolibrary.org/obo/CHEBI_16526" \h   HYPERLINK "http://purl.obolibrary.org/obo/CHEBI_16526" \h http://purl.obolibrary.org/obo/CHEBI_16526 Definition: A one-carbon compound with formula CO2 in which the carbon is attached to each oxygen atom by a double bond. A colourless, odourless gas under normal conditions, it is produced during respiration by all animals, fungi and microorganisms that depend directly or indirectly on living or decaying plants for food. 1.2.1. Atmospheric carbon dioxide Atmospheric carbon dioxide - IRI: TBD Definition: Gas phase carbon dioxide molecules in the air surrounding Earth. A principle contributor to climate change and the main source of carbon used by photoautotrophs to store energy during primary production. 1.3. Fixed carbon Carbohydrate - IRI:  HYPERLINK "http://purl.obolibrary.org/obo/CHEBI_16646" \h http://purl.obolibrary.org/obo/CHEBI_16646 Definition: Any member of the class of organooxygen compounds that is a polyhydroxy-aldehyde or -ketone or a lactol resulting from their intramolecular condensation (monosaccharides); substances derived from these by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom; and polymeric products arising by intermolecular acetal formation between two or more such molecules (disaccharides, polysaccharides and oligosaccharides). Carbohydrates contain only carbon, hydrogen and oxygen atoms; prior to any oxidation or reduction, most have the empirical formula Cm(H2O)n. Compounds obtained from carbohydrates by substitution, etc., are known as carbohydrate derivatives and may contain other elements. Cyclitols are generally not regarded as carbohydrates. 1.3. Fixed carbon Carbohydrate - IRI: HYPERLINK "http://purl.obolibrary.org/obo/IMR_0001657" \h   HYPERLINK "http://www.google.com/url?q=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FIMR_0001657&sa=D&sntz=1&usg=AFQjCNFpm4hl6qAs4kOZxwhTRiD09QKD3A" \h http://purl.obolibrary.org/obo/IMR_0001657 HYPERLINK "http://purl.obolibrary.org/obo/IMR_0001657" \h  Definition: The largest class of organic compounds, including STARCH; GLYCOGEN; CELLULOSE; POLYSACCHARIDES; and simple MONOSACCHARIDES. Carbohydrates are composed of carbon, hydrogen, and oxygen in a ratio of Cn(H2O)n. [database_cross_reference: MeSH:D002241] 1.4. Organism 1.4.1 Organism forms 1.4.1.1 Aquatic organisms 1.4.1.1.1 Plankton 1.4.1.1.1.1. Phytoplankton Phytoplankton - ID:  HYPERLINK "http://purl.bioontology.org/ontology/MESH/D010839" \h http://purl.bioontology.org/ontology/MESH/D010839 Definition: Free-floating minute organisms that are photosynthetic. The term is non-taxonomic and refers to a lifestyle (energy utilization and motility), rather than a particular type of organism. Most, but not all, are unicellular algae. Important groups include DIATOMS; DINOFLAGELLATES; CYANOBACTERIA; CHLOROPHYTA; HAPTOPHYTA; CRYPTOMONADS; and silicoflagellates. 1.5. Ecological community Community - IRI:  HYPERLINK "http://purl.obolibrary.org/obo/PCO_0000002" \h http://purl.obolibrary.org/obo/PCO_0000002 definition: A collection of organisms of at least two different species, living in a particular area. 1.5. Ecological community Ecological community - ID: HYPERLINK "http://ecoinformatics.org/oboe/oboe.1.0/oboe-ecology.owl" \l "EcologicalCommunity" \h   HYPERLINK "http://ecoinformatics.org/oboe/oboe.1.0/oboe-ecology.owl" \l "EcologicalCommunity" \h http://ecoinformatics.org/oboe/oboe.1.0/oboe-ecology.owl#EcologicalCommunity Description: In ecology, a community is an assemblage of two or more populations of different species occupying the same geographical area. (wikipedia) An ecological unit composed of a group of organisms or a population of different species occupying a particular area, usually interacting with each other and their environment. (biology-online.org) Q9: annual rate of net primary production for coastal macroalgae 1. Carbon cycle components 1.1. Carbon flux 1.1.1. Primary production carbon flux 1.1.1.1. Net primary production carbon flux 1.1.1.1.1. Annual net primary productivity (timescale or rate is not specific) 1.4. Organism 1.4.1. Algae Algae - ID: HYPERLINK "http://ecoinformatics.org/oboe/oboe.1.0/oboe-biology.owl" \l "Algae" \h   HYPERLINK "http://www.google.com/url?q=http%3A%2F%2Fecoinformatics.org%2Foboe%2Foboe.1.0%2Foboe-biology.owl%23Algae&sa=D&sntz=1&usg=AFQjCNHR-OGklx_tZVdInd2fuM7PY7fp_w" \h http://ecoinformatics.org/oboe/oboe.1.0/oboe-biology.owl#Algae HYPERLINK "http://ecoinformatics.org/oboe/oboe.1.0/oboe-biology.owl" \l "Algae" \h  Description: A general term for members of several groups of non-flowering, usually photosynthetic, often aquatic, eukaryotic organisms ranging from unicellular to large multicellular forms. They lack true roots, stems and leaves characteristic of terrestrial plants. Most definitions do not include prokaryots (e.g., cyanobacteria). Taxonomically, these belong to several taxonomic groups often classified as Protista (itself a catch-all term), which are mostly phytosynthetic. The singular form, alga, is less common [various sources]. 1.4. Organism 1.4.1 Plant 1.4.1.1. Algae Algae - ID:  HYPERLINK "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl" \l "C86587" \h http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C86587 Definition: Chlorophyll-containing, mainly aquatic eukaryotic organisms lacking true stems and roots and leaves. 1.4. Organism 1.4.1 Kingdom plantae 1.4.1.1 Lower plant 1.4.1.1.1. Algae Algae - ID: HYPERLINK "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl" \l "C86587" \h   HYPERLINK "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl" \l "C86587" \h http://purl.bioontology.org/ontology/SNOMEDCT/15122003 HYPERLINK "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl" \l "C86587" \h  Definition: NA 1.4.1.1.1.1. Salt water algae Salt water algae - ID:  HYPERLINK "http://purl.bioontology.org/ontology/SNOMEDCT/82114006" \h http://purl.bioontology.org/ontology/SNOMEDCT/82114006 Synonym: Seaweed 1.3. Aquatic Habitat 1.3.1 Saline water habitat 1.3.1.1 Marine habitat Marine habitat - Term IRI:  HYPERLINK "http://purl.obolibrary.org/obo/ENVO_00000569" \h http://purl.obolibrary.org/obo/ENVO_00000569 definition: A habitat that is in or on a sea or ocean containing high concentrations of dissolved salts and other total dissolved solids (typically >35 grams dissolved salts per litre). [database_cross_reference: NM:nm] 1.3.1.1. Coastal habitat Coast - Term IRI:  HYPERLINK "http://purl.obolibrary.org/obo/ENVO_00000303" \h http://purl.obolibrary.org/obo/ENVO_00000303 definition: The general region of indefinite width that extends from the sea inland to the first major change in terrain features. [database_cross_reference: USGS:SDTS] Q10: CO2 absorption by the ocean 1. Carbon cycle components 1.1. Carbon flux 1.1.1. Primary production carbon flux 1.1.1.1. Gross primary production carbon flux 1.1.1.2. Net primary production carbon flux 1.1.1.2.1. Annual net primary productivity (timescale or rate is not specific) 1.1.2. Carbon dioxide diffusion Carbon dioxide diffusion - IRI: TBD Definition: The process by which carbon dioxide in the atmosphere moves across a phase boundary and into the ocean. This is a major sink of atmospheric carbon dioxide. Dissolved carbon dioxide subsequently reacts to form carbonic acid, bicarbonate ions, and carbonate ions, leading to ocean acidification. 1.2. Carbon dioxide Carbon dioxide - IRI: HYPERLINK "http://purl.obolibrary.org/obo/CHEBI_16526" \h   HYPERLINK "http://www.google.com/url?q=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_16526&sa=D&sntz=1&usg=AFQjCNGta1AnPWiA1RepVTV8rLlXsCm9Zg" \h http://purl.obolibrary.org/obo/CHEBI_16526 HYPERLINK "http://purl.obolibrary.org/obo/CHEBI_16526" \h  Definition: A one-carbon compound with formula CO2 in which the carbon is attached to each oxygen atom by a double bond. A colourless, odourless gas under normal conditions, it is produced during respiration by all animals, fungi and microorganisms that depend directly or indirectly on living or decaying plants for food. 1.2.1. Atmospheric carbon dioxide Atmospheric carbon dioxide - IRI: TBD Definition: Gas phase carbon dioxide molecules in the air surrounding Earth. A principle contributor to climate change and the main source of carbon used by photoautotrophs to store energy during primary production. 1.3. Environmental system 1.3.1. Biome 1.3.1.1. Aquatic biome 1.3.1.1.1. Marine biome 1.3.1.1.1.1. Ocean biome Ocean Biome - Term IRI:  HYPERLINK "http://purl.obolibrary.org/obo/ENVO_01000048" \h http://purl.obolibrary.org/obo/ENVO_01000048 definition: The ocean biome comprises major bodies of saline water, principal components of the hydrosphere. Approximately 71% of the Earth's surface is covered by ocean, a continuous body of water that is customarily divided into several principal oceans and smaller seas. More than half of this area is over 3,000 metres (9,800 ft) deep. Average oceanic salinity is around 35 parts per thousand (ppt) (3.5%), and nearly all seawater has a salinity in the range of 30 to 38 ppt.[database_cross_reference: Wikipedia:Ocean] [database_cross_reference: PLB:plb] 1.3. Environmental feature 1.3.1. Geographic feature 1.3.1.1 Hydrographic feature 1.3.1.1.1. Water body 1.3.1.1.1.1. Marine water body 1.3.1.1.1.1.1. Ocean Ocean - Term IRI:  HYPERLINK "http://purl.obolibrary.org/obo/ENVO_00000015" \h http://purl.obolibrary.org/obo/ENVO_00000015 definition: Continuous saline-water bodies that surround the continents and fill the Earth's great depressions. 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