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spring_2020_log
January 2020
Notes from Data Supp Webinar, Ontologies and Snags: OBO principles, Protege Pizza ontology reasoning example, OWL exercises also talks about the pizza example
From Elisha: metadata/ontology documentation write ups from our NMDC ontology workshop Docs: Intro to Metadata and Ontology
Planet Microbe:
Tara and Tara Arctic, add Carbonate resources to DP's (to get pH don't add other new terms)
List of new DP to go through:
1- HOT Delong Time-series
2- Amazon continuum
3- C-DEBI mid-range (On hold for now but you can start looking at the terms when you have time)
4- Deep Sediment trap (waiting on Edd Delong)
5-GEOTRACES
6-GEOTRACES Artic
Doing HOT_DeLong_Timedepth_series DP have the following ontology tsv remaining to finish: samples_CTD-BCO-DMO (DONE), samples_niskin_BCO-DMO (DONE), Samples_NCBI, samples_paper
1:1 Bonnie
OSM poster session is till 7pm Wednesday. book flights: to arrive at 9 Sunday, leave Thursday. Use pcard for flight but not for not hotel. Separate reimbursement form for travel which will cover hotel. Travel Expense Report form. Get adobe acrobat and use for official forms. Should have free access.
COMPS
Send out doodle poll Try for Monday 10th Tuesday 11th afternoon Friday 7th. Committee meeting.
For first committee meeting have a tentative timeline in the presentation. Higher level material. Basic description of the chapters, what's in the proposal more like an outline. This is the stuff in progress, tentative timeline for proposal, once finished comps exam here tentative papers and their finishing dates. Aim and sub-aims. Run presentation by Bonnie week ahead. Keep overall introduction, overall aims, subaims, wrapup with timeline. Mention that I'm finishing coursework this semester table with courses and grades.
Try for march 30 - 17 april for oral.
PM
According to http://hahana.soest.hawaii.edu/hot/hot-dogs/bextraction.html hot's chl is Fluorometric Chlorophyll a
HPLC Chlorophyll c1+c2+c3 is chlplus as far as I can tell this only shows up in the HOT-Delong timeseries but if we wanted to really delve into the semantics of chlorophyll concentrations could make everything like chl c1, chlc2 chlc3, chl c total which would have the axioms of all three could be an interesting example of querying but maybe not necessary I think CHEBI is missing some chl c variants but an idea if needed later. HPLC Chlorophyll a is hplc. HPLC Divinyl Chlorophyll a is dvchla. Prochlorococcus is pbact. Synechococcus is sbact. Eukaryotes is ebact.
HPLC Prasinoxanthin is prasino which corresponds to Prasinoxanthin_median in Tara. could maybe add this?
HPLC Diadinoxanthin is diadino in HOT corresponds to Diadinoxanthin_median in Tara
Probably a few more of these. For now just add ones I have envo purls for already in tara pangaea hplc DPs to searchable. same with Phaeophytin and Chlorophyll c3 I think.
PProd: Light-12 is l12
Here is the BCO-DMO link for the CDEBI dataset: https://www.bco-dmo.org/project/635868
The attributes described in BCO-DMO are indeed concentrations --> see the parameter description in https://www.bco-dmo.org/dataset/660489
https://www.thoughtco.com/molarity-and-molality-differences-606117 lol
CCA https://www.youtube.com/watch?v=HLMRA54W4LU, https://www.youtube.com/watch?v=5HFhUPeqsV4
scaling type 1 where the samples sit with respect to the sample variables
scaling type 2 shows where the species are
For the US2ST presentation have a future directions slide about how their are tons of projects which could be harmonized by these concentration of terms. BCO-DMO, ESS-DIVE, DATA ONE, MIxS standard,NERC vocab, SWEET, The Australian GOV concentrations thing from Simon, see the envo issue. Perhaps find some database about water qualities/ecotoxicology (arsenic in drinking water or groundwater etc), Could make the title something like: Toward Semantic Harmonization of Environmental Qualities and Concentrations or similar.
It would be really cool to have an example of querying for envo concentration of terms that are relevant to the nitrogen or phosphorus cycle. query subclasses of nitrogen containing element (or similar in chebi) then using that list of subclasses feed those into the concentration of pattern's CHEBI term and get the results, should get concentration of nitrate, nitrite, nitrate and nitrite, ammonium, urea in liquid water back.
Dependent variables, when you get O2 measurments we need a reference temperature.
Challenges for modelers different missing metadata vaules (just as important as units) want things coming in the same way
Water quality session, many talks about ecosystem restoration. Measuring many of the semantics in the scope of PM: nitrate nitrite, chl a, turbidity NTU. They also measured things like PFAS, ibuprofen, glyphosate. CHEBI has CHEBI:27744 - glyphosate and CHEBI:5855 - ibuprofen, so could make envo concentration of terms for these. PFBS dominant PFAS coumpound (in Galveston bay ecotox study). PFOS, and other emerging contaminants. was a NIEHS superfund research grant, like Ramona's superfund grant perhaps?
To add to ENVO: surface slick accumulates plankton & particles, including microplastics. Hawaii research showing large ingestion of microplastics by larval fish. Important ecosystem 8% or nearshort habitat but havae 50% of nustronic larval fish and 90% of floating plastics -> obvious consequences for bioacumulation of toxins in fish. Would also be the places to concentrate microplastic removal efforts.
ENVO to add: pseudofeces. in relation to talks about mussels & microplastics. In conversation with presenter: pseudofeces is the material which the bivavles excrete through the intake valve without digesting it. Normally feces goes though the other valve.
MPies database metabolomics, functional annotations at protein level (instead of nucleotide level).
From Alise: GMrepo and TerrestrialMetagenomeDB see their platform here
OSM poster link: https://agu.confex.com/agu/osm20/meetingapp.cgi/Paper/656654
From Simon Cox: Defining a water quality vocabulary using QUDT and ChEBI A Harmonized Vocabulary For Water Quality
github command line client https://cli.github.com/
From Ramona/Bonnie review paper about the use of ontologies in support of analysis of megagenomic data.
Their use in in microbial metagenomic data analysis annotate for NCBI, integrating multiple datasets like BCO, use GO to describe the function all enable better understanding of microbial community diversity and function. Cite papers from human microbiome, build environment and soil literature.
https://us2ts.org/program venue: Talley Student Union, State Ballroom (3rd floor)
Keynote: functional owl FUNowl, pretty cool
keynote: james overton ROBOT
keynote: https://comodide.com/ http://ontologydesignpatterns.org/wiki/Main_Page
keynote: owlery4 -> OLW API. used inEBI flybrain
keynote:whelk (like ELK). reimplementation of ELK. k-BOOM from chriss reasoning states (are things equivalent) github.com/balhoff/whelk
keynote: webprotege
keynote: semTK (GE users mostly) make the semantics easier for the engineers.
keynote: cedar semanically enriched metadata system John Graybeal from stanford/bioportal check this out
keynote: semantic arts -> unsilo the databases into rdf models to enable querying. gist upper level ontology for buisness enterprises.
kenote: Jen Hammock [email protected] http://bit.ly/39kO0ln
CEDAR https://metadatacenter.org/ john Graybeal standford.
Json-LD tutorial by Harold Solbig https://github.com/fhircat/fhir_rdf_validator/tree/master/tutorial/us2ts
AnzoGraph.com (like blazegrah) but maybe better.
See this example here and click on the graph view, and select the option to view all relations.
http://ontologydesignpatterns.org/wiki/WOP:2020 and www.praxis-workshop.com
Pier mentioned a biome exchange format which seems similar conceptually to our obo-frictionless dps.
travel expense report for OSM. bonnie will send, include travel id. send to back to admin. https://eforms.fso.arizona.edu/createPdf/6/
Bonnie didn't get the career award
Aim2: technical_note from gigascience about dp and our implementation in pm https://academic.oup.com/gigascience/pages/technical_note but instead of tools make about interoperable data components look at examples of technical_notes from gigascience say what I need to do to make this happen to make the publication happen. What needs to be in the paper. don't need to talk about implementation of CI, focus on frictionless OBO-DPS not tools apps backend etc how they can be used ot implment fair , btw there's an example of them in pm outcomes are the frictionless dp's describe the implementation
Grant: should be using "I" in an DDIG NSF grant. Normally NSF is we but here use I. In the intro for PM use "we" then the rest of it use "I". Style like phd enhancment grant, bonnie will send me an example.
AIM3 doing things quicker frank alyward check his papers out for aim3m, worked for Ed Delong on hot (should be the timeseries data) can take some of what he did and go further on more datasets
cut research team section.
split up questions and hypotheses section amongst the three aims.
Shoot for having the oral exam be the last week of April on Thursday at around 330 for Clay's schedule
from Comprehensive Meta-analysis of Ontology
Annotated 16S rRNA Profiles Identifies Beta
Diversity Clusters of Environmental Bacterial
Communities have a section Salinity as the major driving factor for community assembly? could be cool to recap some of the hypotheses here for AIM3 and approach the issue they way they do in this EMP paper and drill down into questions about what features affect community (such as proteobacteria) composition
press3.mcs.anl.gov/gensc/files/2020/02/mixs_v5.xlsx
Keep this science on schema.org issue on best way to represent ontological terms representing observation types in mind for future follow up, will discuss next meeting.
From Matt Jones: Semantic Sensor Network Ontology the other alignments in that appendix are also useful, and were done by Matt J, Simon, Ramona, Mark, Pier, and a couple of others a while back
Check out and respond to https://github.com/ESIPFed/science-on-schema.org/issues/27 with my aim2 suggestions and coordinate with Mark S.