OBOFoundry
Include sample in core
Note that samples can exist outside biology, so this could be in scicore or investigation-core
+1
This will be useful for the Earth science and operations communities. The basic flow we'll needs semantics for is:
- Create plan (OBI/IAO)
- Set out on expedition (BCO?)
- Enter target environment (ENVO)
- Sample (BCO/OBI)
- Store/preserve sample (BCO/OBI)
- Either
- process in situ
- transport to processing facility and process
- Generate data (OBI/IAO)
- Quality control data (OBI/IAO)
- Analyse data and generate results and information products (OBI/IAO)
- Archive information products in repository (OBI/IAO)
All along the way there will be protocols and plans as well as data exhaust that OBI and IAO semantics would/could/should address.
We'll also need a sizable increase in the qualities being measured (PATO) and the units (UO).
Please see discussions around sample versus specimen and observing versus collecting at BiodiversityOntologies/bco#92 and obi-ontology/obi#969 .
I was assuming the model in core would be very simple. A sample material entity, and possibly a process of sampling (but not clear we need this in core, some kind of general purposes 'investigative process' may be sufficient).
- Pier's outline is spot on.
- absolutely we should not create anything like a 'investigative process'. That road leads to 'biomaterial', 'biological process' and the like. Samples are collected for biopsies in clinical practice for surgery decisions, drug checks for employees, for smog checks by the DMV all without any aspects making them investigational (unless you broaden that definition to be meaningless).
- the 'specimen collection' and 'sample collection' processes in OBI were long discussed and argued over by a broad audience beyond biomedical scientists, so I think they are good candidates for inclusion in the core. If we want to avoid that 'planned process' is a much better parent than 'investigational process'
On Wed, Apr 17, 2019 at 2:27 PM Chris Mungall [email protected] wrote:
I was assuming the model in core would be very simple. A sample material entity, and possibly a process of sampling (but not clear we need this in core, some kind of general purposes 'investigative process' may be sufficient).
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I was told at ICBO 2009 that indeed "investigation" covered everything done in clinical medicine: clinical laboratory tests, radiological studies, etc, etc.
So I have been, as a result, firmly under the impression that "investigation" as understood by OBI, at least, is super broad.
If you want to narrow it for OBO Core, fine, but then that will confuse users of OBO Core who then decide to use OBI.
Bill
On Wed, Apr 17, 2019 at 8:23 PM bpeters42 [email protected] wrote:
- Pier's outline is spot on.
- absolutely we should not create anything like a 'investigative process'. That road leads to 'biomaterial', 'biological process' and the like. Samples are collected for biopsies in clinical practice for surgery decisions, drug checks for employees, for smog checks by the DMV all without any aspects making them investigational (unless you broaden that definition to be meaningless).
- the 'specimen collection' and 'sample collection' processes in OBI were long discussed and argued over by a broad audience beyond biomedical scientists, so I think they are good candidates for inclusion in the core. If we want to avoid that 'planned process' is a much better parent than 'investigational process'
On Wed, Apr 17, 2019 at 2:27 PM Chris Mungall [email protected] wrote:
I was assuming the model in core would be very simple. A sample material entity, and possibly a process of sampling (but not clear we need this in core, some kind of general purposes 'investigative process' may be sufficient).
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.
-- Bjoern Peters Professor La Jolla Institute for Allergy and Immunology 9420 Athena Circle La Jolla, CA 92037, USA Tel: 858/752-6914 Fax: 858/752-6987 http://www.liai.org/pages/faculty-peters
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I'm not sure anyone suggested otherwise.. apologies if my previous comment caused confusion
Chris, assuming you were referring to my comment, I was reacting to this sentence (emphasis mine) from Bjorn's email, where he says things happen in clinical medicine without them being "investigational", but under OBI, they clearly are within scope and "investigational":
"Samples are collected for biopsies in clinical practice for surgery decisions, drug checks for employees, for smog checks by the DMV all *without any aspects making them investigational *(unless you broaden that definition to be meaningless)."
On Fri, Apr 19, 2019 at 12:19 AM Chris Mungall [email protected] wrote:
I'm not sure anyone suggested otherwise.. apologies if my previous comment caused confusion
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I was objecting to the introduction of a new term "investigative process" as written by Chris, quoting: " [...] process of sampling (but not clear we need this in core, some kind of general purposes 'investigative process' may be sufficient)". Because defining what 'investigative' means is not going to be meaningful. And yes, OBI covers all kinds of investigations, and all kinds of processes typically found in them. That doesn't mean that every process in the scope of OBI is exclusively found in investigations.
On Fri, Apr 19, 2019 at 4:03 AM Bill Hogan [email protected] wrote:
Chris, assuming you were referring to my comment, I was reacting to this sentence (emphasis mine) from Bjorn's email, where he says things happen in clinical medicine without them being "investigational", but under OBI, they clearly are within scope and "investigational":
"Samples are collected for biopsies in clinical practice for surgery decisions, drug checks for employees, for smog checks by the DMV all *without any aspects making them investigational *(unless you broaden that definition to be meaningless)."
On Fri, Apr 19, 2019 at 12:19 AM Chris Mungall [email protected] wrote:
I'm not sure anyone suggested otherwise.. apologies if my previous comment caused confusion
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.
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-- Bjoern Peters Professor La Jolla Institute for Allergy and Immunology 9420 Athena Circle La Jolla, CA 92037, USA Tel: 858/752-6914 Fax: 858/752-6987 http://www.liai.org/pages/faculty-peters