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#778 new terms request for Biobank data annotation

general
closed
jzheng
None
5
2016-02-03
2015-09-21
jzheng
No

For Biobank data annotation, we need a couple of new terms of collection of specimen.

Sample family or specimen family
Definition: A collection of specimens that is the output of the material processing and input of the process is the same specimen. For example, aliquoting one specimen to multiple tubes and the collection of the aliquoted specimens are sample family.

Human Sample set or human specimen set
Definition: A collection of specimens that collect from one specific person at one specific time point. For example, on Sept 6, 2015, 3 tubes of blood specimen, 1 tube of urine specimen were collected from patient 1. Then 3 blood specimen and 1 urine specimen called sample set.

This term may be more general like: A collection of specimens that collect from one source at a specific time point with label 'sample set' or 'specimen set'.

The parent term 'collection of specimen' also need to be added.
Definition: An object_aggregate that has as parts two or more specimens.
object_aggregate and (has member only specimen) and (has member min 2 specimen)

It would be nice to have logical axioms associated with the terms. Current I don't have good one and would like to discuss it in the OBI call.

Related

OBI Terms: #778

Discussion

  • Sagar

    Sagar - 2015-10-26

    Ran out of time on OBI call, so adding my comment here:
    1. Human sample set- should we include the "For example..." as part of the curator note rather than the definition.
    *The reason is that human sample set might not include 3 tubes of blood and 1 of urine for every instance, therefore I think it should not be part of the definition (but still important to help understand the concept).

     

    Last edit: Sagar 2015-10-26
  • jzheng

    jzheng - 2015-10-26

    Sagar, Thanks for your comments. That information will be put in the 'example of usage'.

     
  • jzheng

    jzheng - 2015-10-26

    Comments from Bjoern. Add 'specimen set collection process', a subClassOf 'specimen collection process' with output, 'specimen set'.

    In addition, try to avoid using 'object aggregate' since there is granularity issue. We need to consider what is object first when use 'object aggregate'. The object will be changed at different granularity levels.

     

    Last edit: jzheng 2015-10-29
  • jzheng

    jzheng - 2015-10-29

    Based on the discussion in OBI dev call on 10/26/2015. Here are the terms for adding to OBI.

    Term: collection of specimens
    Definition: A material entity that has part two or more specimens.
    Logical axiom (eq): 'material entity' and ('has member' only specimen) and ('has member' min 2 specimen)
    Example of usage: PBMC collected from multiple donors over a course of study

    Term: specimen family
    alternative label: sample family
    Definition: A collection of specimens derived from one common specimen via one or more material processing process(es).
    Logical axiom: collection of specimen and derived from some (specimen and has_role some 'family source specimen role')

    Example of usage: Aliquoting one specimen to multiple tubes and the collection of the aliquoted specimens are a specimen family. Slicing a tissue specimen into multiple sections for microscopy.

    Term: family source specimen role
    Definition: a specimen role that inheres in a specimen that through various material processing results in multiple downstream specimens.
    Editor note: create role to enable axiom in specimen family

    Term: specimen set collection process
    Definition: A specimen collection process that generates multiple specimens from one source (e.g. one organism) during a time period which for the purpose of the study can be considered to be taken at the same sampling time.
    Logical axiom: has_part min 2 specimen collection process and has_specified_output some 'specimen set'
    Example of usage: Collection both blood and urine specimens in one clinical visit; Taking out liver and brain specimens during an autopsy

    Term: specimen set
    Definition: A collection of specimens that is collected from one source (e.g. one organism) during a time period which for the purpose of the study can be considered to be taken at the same sampling time.
    Logical axiom: is_specified_output_of some 'specimen set collection process'
    Example of usage: both blood and urine specimens collected in one clinical visit; liver and brain specimens taken during an autopsy

    Term: human specimen set
    Definition: A specimen set that is collected from one person during a time period which for the purpose of the study can be considered to be taken at the same sampling time.
    Logical axiom: 'specimen set' and derives from' some 'Homo sapiens'

    Definitions and logical axioms updated during the OBI call 2015-11-02

     

    Last edit: jzheng 2015-11-02
  • Ramona Walls

    Ramona Walls - 2015-10-29

    I'm glad to see the new definition for a collection of specimens. That will work well for BCO.

     
  • bjoernpeters

    bjoernpeters - 2015-11-04

    I am proposing alternative primary labels to make them more expressive over set / family

    collection of specimens
    - specimens derived from shared ancestor (above: specimen family)
    - specimens collected in one encounter (above: specimen set)
    - specimens collected longitudinally (not above, but would be a natural addition)

    Bjoern

     

    Last edit: jzheng 2015-11-04
  • bjoernpeters

    bjoernpeters - 2015-11-09

    Proposed term definition: specimens collected longitudinally
    A collection of specimens that was derived from the same source material entity at different time points in order to observe changes in that entity.

     
  • Mathias

    Mathias - 2015-11-09

    I have doubts regarding the 'family source specimen role'. It seems to me that this role in the current representation is realized by the process that actually would create the role (creating aliquots).
    I am not sure that what we try to capture here is a realizable entity. I will think about it and try to provide a solution by Monday Nov 16.

     
  • jzheng

    jzheng - 2015-11-18

    Following terms were added into OBI by Chris on Nov 17, 2015
    collection of specimens
    - specimens derived from shared ancestor
    - specimens collected in one encounter
    - human specimen set
    - specimens collected longitudinally

     
  • Mathias

    Mathias - 2015-11-23

    Here is my proposal for dealing with specimen family and most importantly with family source specimen:

    Term: specimen family creation
    Definition: A specimen collection process that has as its input a specimen and as its output a collection of specimens.
    Logical axiom: collection of specimen and has_specified_input some specimen and has_specified_output some specimen set
    Example of usage: Aliquoting one specimen to multiple tubes, slicing a tissue specimen into multiple sections.

    Term: family source specimen
    Definition: A specimen that is the specified input to a specimen family creation.
    Logical axiom: specimen and is_specified_input_to specimen family creation

    Term: specimen family
    alternative label: sample family
    Definition: A collection of specimens that is the outcome of a specimen family creation .
    Logical axiom: collection of specimen and derived from some (specimen and has_role some 'family source specimen role')

     
  • Mathias

    Mathias - 2015-11-23

    The specimen family axiom is wrong. It needs to be: collection of specimen and is_specified_output_of some specimen family creation

     
  • jzheng

    jzheng - 2015-11-23

    The output of a specimen collection process is specimen. During this process some material entity gain specimen role. So, specimen cannot be the input of this process.

    Term: specimen family creation
    Propose to change the definition to:
    A planned process that has as its input a specimen and as its output a collection of specimens through one or more material processing process(s).
    Propose to add logical axiom:
    has part some 'material processing'

    Discussed on obi call: 2015-11-23

     
  • Ramona Walls

    Ramona Walls - 2015-11-24

    It is really important for BCO to allow a specimen to be the input of a specimen collection process for sub-sampling. Suppose you collect one specimen, then take an aliquot of it, which also results in a specimen. I think it would be confusing to call those different processes, although the latter could certainly be a more specific subclass of the former.

     
    • bjoernpeters

      bjoernpeters - 2015-11-24

      'material portioning' (alt label: 'aliquoting') would be the process of
      splitting something into multiple smaller portions. And that can be done
      with specimens, but wouldn't be considered the 'collection' process.

      On Tue, Nov 24, 2015 at 8:33 AM, Ramona Walls rwalls@users.sf.net wrote:

      It is really important for BCO to allow a specimen to be the input of a
      specimen collection process for sub-sampling. Suppose you collect one
      specimen, then take an aliquot of it, which also results in a specimen. I
      think it would be confusing to call those different processes, although the
      latter could certainly be a more specific subclass of the former.


      Status: open
      Group: general
      Created: Mon Sep 21, 2015 08:29 PM UTC by jzheng
      Last Updated: Mon Nov 23, 2015 05:29 PM UTC
      Owner: jzheng

      For Biobank data annotation, we need a couple of new terms of collection
      of specimen.

      Sample family or specimen family
      Definition: A collection of specimens that is the output of the material
      processing and input of the process is the same specimen. For example,
      aliquoting one specimen to multiple tubes and the collection of the
      aliquoted specimens are sample family.

      Human Sample set or human specimen set
      Definition: A collection of specimens that collect from one specific
      person at one specific time point. For example, on Sept 6, 2015, 3 tubes of
      blood specimen, 1 tube of urine specimen were collected from patient 1.
      Then 3 blood specimen and 1 urine specimen called sample set.

      This term may be more general like: A collection of specimens that collect
      from one source at a specific time point with label 'sample set' or
      'specimen set'.

      The parent term 'collection of specimen' also need to be added.
      Definition: An object_aggregate that has as parts two or more specimens.
      object_aggregate and (has member only specimen) and (has member min 2
      specimen)

      It would be nice to have logical axioms associated with the terms. Current
      I don't have good one and would like to discuss it in the OBI call.


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      --
      Bjoern Peters
      Associate 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

       

      Related

      OBI Terms: #778

  • Mathias

    Mathias - 2015-11-30

    If material portioning of different kinds (aliquoting, slicing tissue) is the only way specimen families are created, then based on Bjoern's suggestion, I'd say we can make 'specimen family creation' a subclass to 'material portioning'.
    If this is not the case, then I'd suggest to tread 'specimen family creation' as an attributive collection of processes of a different type.

     
  • jzheng

    jzheng - 2015-11-30

    I think specimen families can only be generated through 'material processing'. The 'material portioning' is one kind of material process.

    Here is my proposal: change the definition of 'specimen family creation' to:
    A planned process that has as its input a specimen and as its output a collection of specimens through one or more material processing process(s).
    Propose to add logical axiom:
    has part some 'material processing'

    It is still under discussion whether has_part a process is equvilent to subClassOf a process. The question raised in the assay harmonization. We can discuss about it in the call when Bjoern can join.

     
  • Mathias

    Mathias - 2015-11-30

    So, based on today's OBI meeting, the proposal was:

    'specimen family creation'
    Superclass: 'material processing"
    Definition: A material processing that has as its input a specimen and as its output a collection of specimens.
    Logical axiom: 'material processing' and has_specified_input some specimen and has_specified_output some specimen set
    Example of usage: Aliquoting one specimen to multiple tubes, slicing a tissue specimen into multiple sections.

     
  • Chris Stoeckert

    Chris Stoeckert - 2016-02-03

    Discussed on Feb. 2, 2016 call. No objections to adding but two points were raised. Will add this and close the tracker item.
    1. In addition to textual examples, it is helpful for logical axioms to provide an example on how it will be used (i.e. with RDF). The major use case (in my view) is to be able to define and relate specimens in a family to their source.
    2. Specimen family creation as discussed at the beginning of this thread may involve multiple material processings.

     
  • Chris Stoeckert

    Chris Stoeckert - 2016-02-03
    • status: open --> closed
     
  • Chris Stoeckert

    Chris Stoeckert - 2016-02-03

    Terms discussed and agreed upon have been added.

     

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