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thesis pieces
The beginning draft(s) for written sections of my masters thesis. I want to employ a write as I go strategy once I have an application ontology and and data compiled, such that I may iteratively ask competency questions, solve them by querying and write about it. Hence I wish to iteratively add to the written thesis and application ontology.
Lookup author of ontology term
Pre and post-composition of complex classes
Increased illumination of a marine water body
Query processes involving sea ice which may have an effect on phytoplankton blooms
Hunting for knowledge preying upon Eddie
Example GFbio use cases of ontology term requests from the scientific community
For work up to this project see log from 20.10.17
To answer a competancy question such as:
"Can we find the author of an ontology term and if so give me their contact information"
Beginning with a sparql query such as:
PREFIX obo: <http://purl.obolibrary.org/obo/>
SELECT DISTINCT ?x ?label ?author
from <http://purl.obolibrary.org/obo/merged/ENVO>
WHERE
{
?x rdfs:subClassOf obo:ENVO_00002200.
?x rdfs:label ?label.
?x obo:IAO_0000117 ?author .
}
Which gets the term editors of people who contributed to terms which are a subclasses of 'sea ice' ENVO_00002200. This returns a list of links to ORCIDs.
Then to get the contact information from these ORCIDs, we can use the ORCID API tutorial here, to query for the associated emails.
Using a two-legged OAuth authorization request to send a token request to be able to query orcid pages:
curl "Accept: application/json" -d "client_id=APP-NPXKK6HFN6TJ4YYI" -d "client_secret=060c36f2-cce2-4f74-bde0-a17d8bb30a97" -d "scope=/read-public" -d "grant_type=client_credentials" "https://sandbox.orcid.org/oauth/token"
Using the returned token 2bd6d6b7-9438-4a5a-8f87-7e43d6eaac25 I ran the following email retrieving query to get the email address associated with the example ORCID. Code sourced from here.
curl -i -H "Accept: application/vnd.orcid+xml" -H 'Authorization: Bearer 2bd6d6b7-9438-4a5a-8f87-7e43d6eaac25' 'https://api.sandbox.orcid.org/v2.0/0000-0002-9227-8514/email'
returning
<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<email:emails path="/0000-0002-9227-8514/email" xmlns:internal="http://www.orcid.org/ns/internal" xmlns:funding="http://www.orcid.org/ns/funding" xmlns:preferences="http://www.orcid.org/ns/preferences" xmlns:address="http://www.orcid.org/ns/address" xmlns:education="http://www.orcid.org/ns/education" xmlns:work="http://www.orcid.org/ns/work" xmlns:deprecated="http://www.orcid.org/ns/deprecated" xmlns:other-name="http://www.orcid.org/ns/other-name" xmlns:history="http://www.orcid.org/ns/history" xmlns:employment="http://www.orcid.org/ns/employment" xmlns:error="http://www.orcid.org/ns/error" xmlns:common="http://www.orcid.org/ns/common" xmlns:person="http://www.orcid.org/ns/person" xmlns:activities="http://www.orcid.org/ns/activities" xmlns:record="http://www.orcid.org/ns/record" xmlns:researcher-url="http://www.orcid.org/ns/researcher-url" xmlns:peer-review="http://www.orcid.org/ns/peer-review" xmlns:personal-details="http://www.orcid.org/ns/personal-details" xmlns:bulk="http://www.orcid.org/ns/bulk" xmlns:keyword="http://www.orcid.org/ns/keyword" xmlns:email="http://www.orcid.org/ns/email" xmlns:external-identifier="http://www.orcid.org/ns/external-identifier">
<common:last-modified-date>2016-10-26T17:03:35.739Z</common:last-modified-date>
<email:email visibility="public" verified="true" primary="false">
<common:created-date>2016-10-26T17:03:05.707Z</common:created-date>
<common:last-modified-date>2016-10-26T17:03:35.739Z</common:last-modified-date>
<common:source>
<common:source-orcid>
<common:uri>http://sandbox.orcid.org/0000-0002-9227-8514</common:uri>
<common:path>0000-0002-9227-8514</common:path>
<common:host>sandbox.orcid.org</common:host>
</common:source-orcid>
<common:source-name>Sofia Maria Hernandez Garcia</common:source-name>
</common:source>
<email:email>[email protected]</email:email>
</email:email>
</email:emails>
From which we can grep out: <email:email>[email protected]</email:email>
Unfortunately I can't yet get this to work with different ORCID's (mine or Piers) perhaps continue here. I emailed the ORCID support with these questions to see if they can help answer this question. For now this is proof of concept for a way to answer the competency question.
Illustrate how with semantic research we can defining complex envo classes such
and
I will do it once as a pre-composition where I push and get an iri for the whole class. Then I will illustrate how to post-compose such classes using pieces from other classes as building blocks to illustrate how it can be done either way.
To answer the following competency question:
"What processes result in increased illumination of a marine water body?"
Making use of the ENVO class sea ice melting which contains the axioms ... we are able to perform the following query ... to give us any process which affects the illumination state of a water body. The query returns the sea ice melting class.
see issue 13
Get Eddie's input for hole in the ice bloom class plus some of the useful microbial communities for his work. Perhaps I could even use some of his 16 rRNA data for my pulled together dataset.
From Eddie's input the hole in the ice bloom class would be something along the lines of ice free zone in ice-covered region He will also send me his ORCID so I can put it on the PCO classes. The 16s data should be published by the end of the year so it should be available for use it for the thesis.
include releases from lab rotation