smrgeoinfo
commented
9 years ago Deconstruct and focus on plotting found sample locations in Paleocoordinates. Task @smrazgs -- compare and contrast this as a processing use case with the tree ring use case. Shanan Peters is domain point guy.
Use Case: Stratigraphy: Get the stable isotopic measurements, from carbonates in North America of Silurian age, integrate them with all known fossil occurrences and geochronological estimates and rotate all of the data back to their proper paleocoordinates.
2015-03-04 SMR at user meeting-- simplify to just finding samples of Silurian age with Oxygen or Carbon stable isotope measure and reprojecting sample locations to Silurian paleocoordinates.
Analysis
Text parse
‘stable isotope’ == phenomonon Add isotopes for each element. Each isotope has a half life. Stable isotope is > X halflife Want any stable isotope? ‘get...measurement’ => return table of observations ‘carbonate’ == shorthand for ‘carbonate EarthMaterial’, but probably means ‘carbonate rock’ ‘carbonates in North America’ == SamplingFeature.composition.lithology = ‘carbonate rock’ ‘Silurian Age’ == time ordinal era from geologic time scale; there are various slightly different versions of Silurian, assume ICS 2012? Need concept expansion to allow for subdivisions of Silurian. ‘integrate’== associate with related resources. source is observation, target is a feature occurrence. There are a large variety of possible relationships between an observation and a feature occurrence. ‘fossil’ == a feature type that has an associated biological organism. ‘fossil occurrence’ == a particular instance of a fossil feature, situated in a particular context (geologic unit, geographic location...) ‘geochronologic estimate’ == interpret this to mean an estimated temporal coordinate (numeric) of some geologic event. Typical example would be event=crystallization of magma. This is an observation result value. Geochronologic estimates (‘age dates’) are normally associated with a geologic specimen that has a geographic location (samplingFeature.extent) and stratigraphic context (samplingFeature.featureOfInterest.GeologicUnit).
Queries:
Find datasets that have stable isotope observation results, specify the samplingFeature.material.lithology, and specify samplingFeature.geoogicUnit.age For Each Dataset find observations: Sample material = carbonate rock AND Analyte = stable isotope AND Geologic unit age = silurian (sample probably associated with Geologic unit, Geologic unit should be associated with an age) get list of analyses, for each analysis there is a sample, each sample has a location.. get sample Location Fossil occurrences near analyzed sample in same geologic unit. list of fossils, each with a collection location (collection locations may be obfuscated) Using fossil taxa, and collection location: Geochron: could look for age dates near the collection location for the fossils-- if the date is in the same unit as the fossil, provide a bigger envelope (10 km); if the date is from a different unit, then the search envelop is smaller (1 km?). Get bunch of geochron sample locations and results for all sample locations, plug into service that returns Silurian paleocoordinates.
Other Notes
From Ilya, 12/1/2014
Thanks Shanan, Get the stable isotopic measurements, described previously, integrate them with all known fossil occurrences and geochronological estimates and rotate all of the data back to their proper paleocoordinates.
If we try to deconstruct this query: 1) Do you have a preferred vocabulary/ontology for stable isotopes? Ideally, anything better organized than http://www.periodictable.com/Properties/A/StableIsotopes.html orhttp://chemistry.wikia.com/wiki/List_of_stable_isotopes ? 2) How likely is it to navigate to useful data from the “measurement” keyword – ie looking for documents/datasets that used isotope ratio mass spectrometry? 3) Fossil occurrences – would you say that http://fossilworks.org/ is the place to search, or there are other (better) places? 4) Geochronological estimates: do you use http://mrdata.usgs.gov/geochron/? 5) Is https://www.seegrid.csiro.au/wiki/AnalyticalGeoscience/Geochronology something you use? It is attractive because it is based on the O&M, which several geo-related data models are also based on 6) For the paleocoordinates output, we should at least be able to point to GPlates.org and tohttp://www.scotese.com/software.htm ? Any other software that should be returned on searching for “paleo and coordinates”?
For each of them, CINERGI would return APIs and any other metadata that would support integration (to the extent available in metadata or added by the CINERGI pipeline). This is an interesting use case, let’s see how far we can move towards a useful solution. I cc to Steve and Amarnath on our team.
From Shanan Peters, 12/1/2014
1,2) Stable carbon isotopes are referred to with a rather limited vocabulary, though one that does involve potentially different standards and that does require knowledge of what phase/component was analyzed. 3) fossilworks = paleobiodb.org (latter is preferred) 4) This is a great starting point. 5) I don’t know much about this system/resource. 6) GPlates = ideal starting point