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Social Ontology and the Biomedical Domain

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Division of Biomedical Informatics. Problems in Ontology. October 10, 2012. Contents. From demographics to OMRSE. ... Health care. Banking. Retail. Government ... – PowerPoint PPT presentation

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Title: Social Ontology and the Biomedical Domain


1
Social Ontology and the Biomedical Domain
  • M. Brochhausen, W.R. Hogan
  • Division of Biomedical Informatics
  • Problems in Ontology. October 10, 2012

2
Contents
  • From demographics to OMRSE
  • Intro
  • Sex vs. Gender
  • Marital status
  • Technical details of OMRSE
  • The problem of organizations
  • Document act ontology
  • Example Clinical guidelines

3
1. From demographics to OMRSE
  • Motivation
  • Demographics are important
  • But there are problems
  • No interoperability few standards widely
    adopted
  • Current approaches have flaws

4
The importance of demographics
  • Ubiquitous in information systems in
  • Health care
  • Banking
  • Retail
  • Government (especially census)
  • Useful for
  • Identifying people
  • Comparing populations
  • Linking records from multiple databases

5
Problems with current approaches
  • No ontological distinctions
  • All demographics are attributes related to the
    person in exactly the same way
  • Require fields/attributes/properties that are
    specific to demographics
  • Do not represent as first-order entities
  • Even semantic web uses data type properties
  • Cannot say anything else about birth, birthday,
    gender, martial status, or changes over time
  • Confuse sex and gender

6
Interoperability in current approaches
  • Requires shared field/attribute names as well as
    standard codes for coded attributes
  • Semantic web
  • Different URIs for same property
  • FOAF http//xmlns.com/foaf/0.1/birthday
  • vCARD http//www.w3.org/2006/vcard/nsbday
  • For gender in FOAF, no interoperability of values
  • Any string is compliant M, m, male,
    mael, masculine are all valid
  • So how can we reliably query for persons of male
    gender?

7
Problems with current approaches
from a data dictionary for emergency data that is
actually in use
8
Gender Refers to the socially constructed roles, behaviours, activities, and attributes that a given society considers appropriate for men and women. Social Role
Sex Refers to the biological and physiological characteristics that define men and women. Biological Quality
Quoted from http//www.who.int/gender/whatisgende
r/en/index.html
9
Gender in OMRSE
  • Gender represented as a role in human social
    processes
  • based on BFO

10
Sex in PATO
  • Sex represented as an organismal quality
  • Reused in BFO-based ontologies, for instance OBI

11
Our method for analysis
  • Identify the relevant particulars in reality
  • Determine the types they instantiate
  • Identify the relations that hold among them
  • Create new representations of types in ontologies
    as needed

12
Marital status
  • Entities
  • jd_mc_role J. Does party to marriage contract
    role
  • t3 Instant at which marriage contract
    begins to exist
  • Instantiations
  • jd_mc_role instance_of Party to a marriage
    contract since t3
  • t3 instance_of Temporal instant
  • Relations
  • jd bearer_of jd_mc_role since t3

The paper also shows how to represent the fact
that no such a role inheres in a person to
capture single
13
Marital status based on OMRSE
  • represented as role
  • based on BFO

14
Marital status under construction
  • Claims and obligations that are the grounding of
    the role party to a marriage contract
  • Challenge representation of legal entities in
    BFO
  • Will be based on document act ontology

15
2. Technical details of OMRSE
  • written in OWL2
  • based on BFO 1.1
  • 116 classes, 7 object properties
  • so far all classes are subclass to continuant
  • project home http//code.google.com/p/omrse
  • download https//purl.obolibrary.org/obo/omrse.ow
    l

16
2. Technical details of OMRSE
  • agreement with Ontology of Biomedical
    Investigation (OBI) to take responsibility for
    its domain
  • still in (relatively) initial state
  • still needs to take over some entities from OBI
    for curation (e.g. organization)

17
3. The problem of organizations
18
Ontological issues
  • _at_SMcC_TheDetail Does this mean every EU citizen
    is now a Nobel prize winner. That'll look good on
    the CV!
  • Are states organizations?
  • Membership vs. citizenship
  • Joint agency joint passivity?

19
Definition of organization in OBI
  • An organization is a continuant entity which can
    play roles, has members, and has a set of
    organization rules. Members of organizations are
    either organizations themselves or individual
    people. Members can bear specific organization
    member roles that are determined in the
    organization rules. The organization rules also
    determine how decisions are made on behalf of the
    organization by the organization members.
  • https//purl.obolibrary.org/obo/obi.owl

20
Problems with OBI's representation of
organization
  • Ambiguity regarding the difference between groups
    and formal organizations.
  • Are "rules" explicit?
  • Omission of the processual foundation of (formal)
    groups, e.g. on document acts.
  • no formal definition
  • Intra-organizational procedures and structures
    are not (yet) represented.
  • Do we assume group intentions?

21
4. Document act ontology and clinical guidelines
from Scottish Intercollegiate Guidelines
Network www.sign.ac.uk
22
How do sentences/documents create obligations or
rights?1
  • Sentences and documents create obligations and
    claims all the time (Examples Guidelines create
    obligations in specific contexts, prescriptions
    create claims, etc.)
  • Even though language is used for the creation of
    the obligation, it is independent of language.
  • 1 I am presenting work done collaboratively with
    Laura Slaughter and Mauricio Almeida.

23
"Sell Mr. Harris 20 units of 0.5 mg Lorazepam."
  • Written in a novel, read by Jane Doe
  • no claim created
  • Uttered by me right now
  • no claim created
  • written on a prescription signed by an authorized
    doctor delivered to a pharmacist
  • in the signing process a claim was created

24
  • In order to capture these contextual aspects we
    need to resort to some kind of speech act theory.

"social acts"
"document acts"
25
Document act
  • "Through the performance of document acts (acts
    of filling in, registering, conveying,
    validating, attaching) we change the world by
    bringing into being ownership relations, legal
    accountability, business organizations, and a
    variety of other institutional orders of modern
    societies."
  • (Smith, 2008)

26
OWL Implementation
  • Based on Basic Formal Ontology (BFO)
  • Imported classes- Information Artifact Ontology
    (IAO)
  • Available on Google Project Hosting
  • http//code.google.com/p/d-acts/

ALMEIDA MB, SLAUGHTER L, BROCHAUSEN M (2012).
Towards an ontology of document acts Introducing
a document act template for healthcare. OTM 2012
Workshops, LNCS 7567, pp. 420425.
27
2.2.Document act
Types
document
document act
rights/obligations
has specified input
has specified output
Clinical guideline document
Ratification of a guideline by a hospital
organization
Obligation to follow the guideline in question
Instances
28
Clinical Guidelines and Organizations
www.guidelines.gov
29
Search results for breast cancer, screening,
mammography (9 out of 20)
30
Guideline content
  • "() the College recommends that women aged 40
    years and older be offered screening mammography
    annually."
  • "The screening frequency for mammography is every
    one to two years."
  • "The USPSTF recommends biennial screening
    mammography for women aged 50 to 74 years."

31
Three guidelines, three different individual
organizations and three different types of
organizations
32
  • Guideline 1
  • American College of Obstetricians and
    Gynecologists
  • ACOG Committee on Practice Bulletins-Gynecology
  • Committee created by College, Members of
    Committee elected by the Committee President
  • Guideline 2
  • Kaiser Permanente Care Management Institute
  • Breast Cancer Screening Guideline Development
    Team
  • Not specified
  • Guideline 3
  • U.S. Preventive Services Task Force
  • U.S. Preventive Services Task Force
  • Members of TF appointed by Director of the Agency
    for Healthcare Research and Quality

33
  • It would be helpful to understand the internal
    structures underlying the guidelines committee.
    This would users insight into the trustworthiness
    and authority of individual guidelines.
  • To achieve that one needs a formal representation
    of the structures of the organizations mentioned.
  • So far most organization ontologies are nothing
    more but structured lists of individual
    organizations.

34
ACOG
Professional Association
Guideline 1
ACOG Committee President
ACOG Committee
ACOG Committee
Government Organization
Guideline 1
US PSTF
AHRQ
35
Acknowledgments
  • Swetha Garimalla, Tariq Shariq (OMRSE)
  • Mauricio B. Almeida, Laura Slaughter (d-acts)
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