Wiki page for the work on the Planet Microbe project.

Link to basecamp folder

Link to google docs mapping metadata from the projects to ontology terms.

Link to draft of Planet Microbe paper

Planet_microbe_ontology_terms

Wiki Page for the management and creation of new OBO ontology terms by which to annotate planet microbe metadata, as well as aid to standardize the commonly used metadata for the marine microbiology & oceanography communities.

Created google spread sheet for the Automated term creation

Terms to Create:

Manual term creation

PATO:

alkalinity

turbidity

//subclass of 'opacity'

salinity

An osmolarity quality inhering in a bearer by virtue of the bearer's amount of solute, composed primarily of dissolved ionic compounds, per liter of solution.

is a osmolarity

dbxref1, dbxref2,

ENVO:

Manual term creation

concentration of nitrate and nitrite in water

//synonym NOX 'nitrate' 'nitrite' 'sea water'

alkalinity of water

['alkalinity'](no purl yet) 'water'

salinity of water

A salinity quality inhering in water by virtue of that water's amount of salt content per volume.

[salinity](no purl yet) and ('inheres in' some ('salt' and ('part of' some 'water')))

turbidity of water

['turbidity'](no purl yet) 'water'

concentration of bacteria in water

This may refer to any microorganism not just bacteria perhaps just prokaryotes but maybe also small eukaryotes double check this. 'Bacteria' 'water'

Automated term creation

entity_attribute_location design pattern

Making use of the pattern from the design pattern script entity_attribute_location.yaml and data csv entity_attribute_location.csv

concentration of classes

'concentration of' and ('inheres in' some (X and ('part of' some Y)))

concentration of ammonium in water

'ammonium' 'water'

concentration of chlorophyll a in water

'chlorophyll a' 'water'

concentration of chlorophyll b in water

'chlorophyll b' 'water'

concentration of chlorophyllide a in water

'chlorophyllide a' 'water'

concentration of bacteriochlorophyll a in water

'bacteriochlorophyll a' 'water'

concentration of alloxanthine in water

'alloxanthine' 'water'

concentration of peridinin in water

'peridinin' 'water'

concentration of carotene in water

'carotene' 'water'

concentration of alpha-carotene in water

'alpha-carotene' 'water'

concentration of beta-carotene in water

'beta-carotene' 'water'

concentration of divinyl chlorophyll a in water

'divinyl chlorophyll a' 'water'

concentration of divinyl chlorophyll b in water

'divinyl chlorophyll b' 'water'

concentration of neoxanthin in water

'neoxanthin' 'water'

concentration of fucoxanthin in water

'fucoxanthin' 'water'

concentration of adenosine triphosphate in water

'Adenosine 5'-triphosphate' 'water'

concentration of guanosine triphosphate in water

'Guanosine 5'-triphosphate' 'water'

concentration of hydrogen peroxide in water

'hydrogen peroxide' 'water'

concentration of hydrogen sulfide in water

'hydrogen sulfide' 'water'

concentration of methane in water

'methane' 'water'

concentration of lutein in water

'lutein' 'water'

concentration of violaxanthin in water

'violaxanthin' 'water'

concentration of zeaxanthin in water

'zeaxanthin' 'water'

concentration of nitrate in water

'nitrate' 'water'

concentration of nitrite in water

'nitrite' 'water'

concentration of nitrous oxide in water

'nitrous oxide' 'water'

concentration of oxygen in water

'dioxygen' 'water'

concentration of phosphate in water

'phosphate' 'water'

concentration of prochlorococcus in water

'Prochlorococcus' 'water'

concentration of silicate in water

'silicate(4-)' 'water'

concentration of synechococcus in water

'Synechococcus' 'water'

**additional terms not in the original datasets but which may show up in oceanography/microbial ecology measurements:

concentration of nitric oxide in water

nitric oxide 'water'

concentration of sulfate in water

sulfate 'water'

concentration of hydrogen sulfide in water

hydrogen sulfide 'water'

concentration of methane in water

methane 'water'

add iron and manganese next

entity_attribute design pattern

The following use the entity_attribute.yaml design pattern, with entity_attribute.csv data csv. Which was responsible for the creation of the example class acidity of soil or conductivity of soil.

acidity of water

'acidity' 'water'

conductivity of water

'conductivity' 'water'

depth of water

'depth' 'water'

fluorescence of water

'fluorescence' 'water'

pressure of water

'pressure' 'water'