Towards an ontological treatment of disease and diagnosis
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Towards an Ontological Treatment of Disease and Diagnosis. Barry Smith New York State Center of Excellence in Bioinformatics and Life Sciences University at Buffalo.

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Towards an ontological treatment of disease and diagnosis

Towards an Ontological Treatment of Disease and Diagnosis

Barry Smith

New York State Center of Excellence in Bioinformatics and Life Sciences

University at Buffalo

http://ontology.buffalo.edu/smith


Towards an ontological treatment of disease and diagnosis

Anders Grimsmo, “Patients, diagnoses and processes in general practice in the Nordic countries. An attempt to make data from computerised medical records available for comparable statistics”Scandinavian Journal of Primary Health Care, 2001

  • “The major obstacle to extracting more epidemiological data from computerised medical records is caused by information in the databases not being uniquely linked to episodes of care.”

http://ontology.buffalo.edu/smith


What is to be linked with what

What is to be linked with what?

What is information in the databases about?

To answer this question (to assign numbers to discrete entities), we need a good ontology of the care domain, including episodes of care on the one hand and entities on the side of the patient on the other.

http://ontology.buffalo.edu/smith


And we need to take account of context

and we need to take account of context

– of multiple diseases

– of the patient’s style of life

– of the patient’s environment

– of specific aspects of the presentation

http://ontology.buffalo.edu/smith


We do this by paying attention to natural language

we do this by paying attention to natural language

but the more we succeed in this, the more difficult it is to aggregate the data

disease of UMLSitis

http://ontology.buffalo.edu/smith


Towards an ontological treatment of disease and diagnosis

OBO Foundry


Towards an ontological treatment of disease and diagnosis

Buffalo Longitudinal Cancer Data

Even with the best of intentions, and even if we just use one coding system, results are not always what they seem

Problem of SNOMEDitis

with acknowledgements to NLM: 1R21LM009824-01A1


Why does snomed change so much

Why does SNOMED change so much?


Towards an ontological treatment of disease and diagnosis

SNOMED CT: Anaplasmamarginale (organism)

with acknowledgements to

NLM: 1R21LM009824-01A1


Towards an ontological treatment of disease and diagnosis

infectious agent

is_a navigational concept

with acknowledgements to

Werner Ceusters

NLM: 1R21LM009824-01A1


Towards an ontological treatment of disease and diagnosis

infectious agent

is_a navigational concept


Towards an ontological treatment of disease and diagnosis

with acknowledgements to

NLM: 1R21LM009824-01A1


Towards an ontological treatment of disease and diagnosis

with acknowledgements to

NLM: 1R21LM009824-01A1


Towards an ontological treatment of disease and diagnosis

with acknowledgements to

NLM: 1R21LM009824-01A1


Towards an ontological treatment of disease and diagnosis

with acknowledgements to

NLM: 1R21LM009824-01A1


Why does snomed change so much1

Why does SNOMED change so much?

Problems with ‘concept’  no real coherence as to what SNOMED is representing


Why does snomed change so much2

Why does SNOMED change so much?

No proper hierarchy (of more and less general)

Confusion of disorders (continuants) with etiological and diagnostic processes (occurrents) and of both with information entities (‘findings’)

Confusion of ‘disorders’ with ‘morphological abnormalities’


Snomed ct

SNOMED CT

128477000 Abscess (disorder)

44132006 Abscess (morphologic abnormality)


Epistemology and combinatorial explosion

Epistemology and Combinatorial Explosion

  • Epistaxis/nosebleed

    • Epistaxis (disorder)

    • Nosebleed/epistaxis symptom (finding)

    • On examination - epistaxis (disorder)

    • Has nosebleeds - epistaxis (disorder)

    • Evidence of recent epistaxis (finding)

      from Bill Hogan


Epistemology and combinatorial explosion1

Epistemology and Combinatorial Explosion

  • Rash

    • Cutaneous eruption (morphologic abnormality), with synonym Rash

    • Eruption of skin (disorder), with synonym Rash

    • Complaining of a rash (finding)

    • On examination - a rash (finding)

  • Dry skin

    • Dry skin (finding)

    • Complaining of dry skin (finding)

    • On examination - dry skin (finding)

    • Dry skin dermatitis (disorder)

      from Bill Hogan


An alternative basic formal ontology

An Alternative: Basic Formal Ontology

  • 360 BC: Aristotle’s Metaphysics

  • 1879: Invention of modern logic (Boole,

  • Frege)

  • 1920:The problem of the Unity of Science (Logical Positivism)

  • 1940Birth of computing (Turing)

http://ontology.buffalo.edu/smith


Ontology timeline

Ontology Timeline

  • 1970: AI, Robotics (J. McCarthy, P. Hayes)

  • 1980:KIF: Knowledge Interchange Format

  • 1990: Description Logics

  • 2000: Semantic Web (OWL), Protégé

  • 2007: National Center for Biomedical Ontology (NCBO) Bioportal

http://ontology.buffalo.edu/smith


Uses of ontology in pubmed abstracts

Uses of ‘ontology’ in PubMed abstracts


Towards an ontological treatment of disease and diagnosis

Biomedical Ontology in PubMed


Towards an ontological treatment of disease and diagnosis

By far the most successful: GO (Gene Ontology)


Ontology timeline1

Ontology Timeline

  • 1990: Human Genome Project

  • 1999: The Gene Ontology (GO) – Model Organism Research

  • 2005: The Open Biomedical Ontologies

  • (OBO) Foundry

  • 2010: Ontology for General Medical

  • Science

http://ontology.buffalo.edu/smith


The go is a controlled vocabulary for use in annotating data

The GO is a controlled vocabulary for use in annotating data

  • multi-species, multi-disciplinary, open source

  • contributing to the cumulativity of scientific results obtained by distinct research communities

  • compare use of kilograms, meters, seconds … in formulating experimental results


Towards an ontological treatment of disease and diagnosis

NIH Mandates for Data Sharing

Organizations such as the NIH now require use of common standards in a way that will ensure that the results obtained through funded research are more easily accessible to external groups.

ODR will be created in such a way that its use will address the new NIH mandates. It will designed also to allow information presented in its terms to be usable in satisfying other regulatory purposes—such as submissions to FDA.

http://ontology.buffalo.edu/smith


Go provides answers to three types of questions

GO provides answers to three types of questions:

for each gene product (protein ...)

  • in what parts of the cell has it been identified? Cell Constituent Ontology

  • exercising what types of molecular functions? Molecular Function Ontology

  • with what types of biological processes? Biological Process Ontology


Towards an ontological treatment of disease and diagnosis

  • = part_of

  • = subtype_of

  • Gene Product

  • Associations


100 mill invested in literature curation using go

$100 mill. invested in literature curation using GO

over 11 million annotations relating gene products described in the UniProt, Ensembl and other databases to terms in the GO

ontologies provide the basis for capturingbiologicaltheories in computable form

in contrast to terminologies and thesauri – which focus on socially diverse uses of language – the GO methodfocuses on commonlysharedresults of basic biological science


Towards an ontological treatment of disease and diagnosis

A new kind of biological researchbased on analysis and comparison of the massive quantities of annotations linking ontology terms to raw data, including genomic data, clinical data, public health dataWhat 10 years ago took multiple groups of researchers months of data comparison effort, can now be performed in milliseconds


The go covers only generic normal biological entities of three sorts

The GO covers only generic (‘normal’) biological entities of three sorts:

  • cellular components

  • molecular functions

  • biological processes

    It does not provide representations of diseases, symptoms, genetic abnormalities …

    How to extend the GO methodology to other domains of biology and medicine?


Towards an ontological treatment of disease and diagnosis

The Open Biomedical Ontologies (OBO) Foundry


Obo foundry ontologies

OBO Foundry ontologies

all follow the same principles to ensure interoperability

  • GO Gene Ontology

  • ChEBI Chemical Ontology

  • PRO Protein Ontology

  • CL Cell Ontology

  • ...

  • OGMS Ontology for General Medical Science


Basic formal ontology go at a high level

Basic Formal Ontology: GO at a high level

http://ontology.buffalo.edu/smith


Basic formal ontology bfo

Basic Formal Ontology (BFO)

A simple top-level ontology to support information integration in scientific research

No abstracta

Nothing propositional

Clear hierarchy

No overlap with domain ontologies

No confusion of ontology with epistemology

No confusion of terms with what terms represent in reality


Basic formal ontology

Basic Formal Ontology

Continuant

Occurrent

(Process, Event)

Independent

Continuant

Dependent

Continuant

http://ifomis.uni-saarland.de/bfo/


Bfo and the 3 gene ontologies go

BFO and the 3 Gene Ontologies (GO)

Continuant

Occurrent

Biological Process

Independent

Continuant

Dependent

Continuant

Cell Component

Molecular Function

Kumar A., Smith B, Borgelt C. Dependence relationships between Gene Ontology terms based on TIGR gene product annotations. CompuTerm 2004, 31-38.

Bada M, Hunter L. Enrichment of OBO Ontologies. J Biomed Inform. 2006 Jul 26


Users of bfo

Users of BFO

NCI BiomedGT

SNOMED CT

Ontology for General Medical Science (OGMS)

ACGT Clinical Genomics Trials on Cancer – Master Ontology / Formbuilder (Case Report Forms for Cancer Clinical Trials)


Users of bfo1

Users of BFO

MediCognos / Microsoft Healthvault

Cleveland Clinic Semantic Database in Cardiothoracic Surgery

Major Histocompatibility Complex (MHC) Ontology (NIAID)

Neuroscience Information Framework Standard (NIFSTD) and Constituent Ontologies


Users of bfo2

Users of BFO

Interdisciplinary Prostate Ontology (IPO)

Nanoparticle Ontology (NPO): Ontology for Cancer Nanotechnology Research

Neural Electromagnetic Ontologies (NEMO)

ChemAxiom – Ontology for Chemistry

Ontology for Risks Against Patient Safety (RAPS/REMINE) (EU FP7)

IDO Infectious Disease Ontology (NIAID)


Infectious disease ontology consortium

Infectious Disease Ontology Consortium

  • MITRE, Mount Sinai, UTSouthwestern – Influenza

  • IMBB/VectorBase – Vector borne diseases (A. gambiae, A. aegypti, I. scapularis, C. pipiens, P. humanus)

  • Colorado State University – Dengue Fever

  • Duke University – Tuberculosis, Staph. aureus

  • Case Western Reserve – Infective Endocarditis

  • University of Michigan – Brucellosis


The obo foundry

The OBO Foundry

  • GO Gene Ontology

  • CL Cell Ontology

  • SO Sequence Ontology

  • ChEBI Chemical Ontology

  • PATO Phenotype (Quality) Ontology

  • FMA Foundational Model of Anatomy

  • ChEBI Chemical Entities of Biological Interest

  • CARO Common Anatomy Reference Ontology

  • PRO Protein Ontology

  • Infectious Disease Ontology

  • Plant Ontology

  • Environment Ontology

  • Ontology for Biomedical Investigations

  • RNA Ontology  


Towards an ontological treatment of disease and diagnosis

The Open Biomedical Ontologies (OBO) Foundry


Towards an ontological treatment of disease and diagnosis

RELATION TO TIME

GRANULARITY

rationale of OBO Foundry coverage (homesteading principle)


Obo foundry organized in terms of basic formal ontology

OBO Foundry organized in terms of Basic Formal Ontology

Methodology of downward population

Each Foundry ontology can be seen as an extension of a single upper level ontology (BFO)


Example the cell ontology

Example: The Cell Ontology


Ontology for general medical science bfo based ontology for clinical m edicine

Ontology for General Medical Science BFO-based ontology for clinical medicine

Continuant

Occurrent

Pathological Process

+

Clinical Encounter

Independent

Continuant

Dependent

Continuant

Anatomical Component

+

Disorder

Disease

+

Bodily Quality


Towards an ontological treatment of disease and diagnosis

Continuant

Independent

Continuant

Dependent

Continuant

Quality

Disposition

..... .....


Realization depends on realizable

realization depends_on realizable

Continuant

Occurrent

Independent

Continuant

bearer

Dependent

Continuant

disposition

Process of

realization

.... ..... .......


Towards an ontological treatment of disease and diagnosis

the universal eye

the universal red

instantiates

instantiates

this particular case of redness (of a particular fly eye)

an instance of eye (in a particular fly)

depends_on


Towards an ontological treatment of disease and diagnosis

color

anatomical structure

is_a

is_a

red

eye

instantiates

instantiates

an instance of an eye (in a particular fly)

the particular case of redness (of a particular fly eye)

depends on


Towards an ontological treatment of disease and diagnosis

Phase transitions

portion of water

portion of ice

portion of liquid water

portion of gas

instantiates at t1

instantiates at t2

instantiates at t3

this portion of H20


Towards an ontological treatment of disease and diagnosis

human

in nature, no sharp boundaries here

embryo

fetus

neonate

infant

child

adult

instantiates at t1

instantiates at t2

instantiates at t3

instantiates at t4

instantiates at t5

instantiates at t6

John (exists continuously)


Towards an ontological treatment of disease and diagnosis

temperature

in nature, no sharp boundaries here

in nature, no sharp boundaries here

37ºC

37.1ºC

37.2ºC

37.3ºC

37.4ºC

37.5ºC

instantiates at t1

instantiates at t2

instantiates at t3

instantiates at t4

instantiates at t5

instantiates at t6

John’s temperature (exists continuously)


Towards an ontological treatment of disease and diagnosis

coronary heart disease

early lesions and small fibrous plaques

asymptomatic (‘silent’) infarction

surface disruption of plaque

unstable angina

stable angina

instantiates at t1

instantiates at t2

instantiates at t3

instantiates at t4

instantiates at t5

John’s coronary heart disease (exists continuously)

time


Towards an ontological treatment of disease and diagnosis

OGMS

Ontology for General Medical Science

http://code.google.com/p/ogms/


Ogms the big picture

OGMS: The Big Picture


Disposition potentiality

Disposition (potentiality)

A disposition is

a realizable entity which is such that, if it ceases to exist, then its bearer is physically changed,

whose realization occurs, in virtue of the bearer’s physical make-up, when this bearer is in some special physical circumstances


Disorder

Disorder

independent continuant

that is part of an organism

that deviates from the canonical anatomy of the organism

in a way that gives rise to pathological processes


Disorder1

Disorder

serves as the bearer of a disposition to pathological processes

A part of the body that typically gets larger over time


Disease course

Disease course

  • the totality of all disease processes through which a given disease instance is realized .

  • multiple disease courses will be associated with the same disorder type, for example in reflection of the presence or absence of pharmaceutical or other interventions, of differences in environmental influence, and so forth.


The big picture

The Big Picture


Towards an ontological treatment of disease and diagnosis

A disease is a disposition rooted in a

physical disorder in the organism and

realized in pathological processes.

produces

bears

realized_in

etiological process

disorder

disposition

pathological process

produces

diagnosis

interpretive process

signs & symptoms

abnormal bodily features

produces

used_in

recognized_as


Definitions foundational terms

Definitions - Foundational Terms

  • Disorder =def. – A causally linked combination of physical components that is clinically abnormal.

  • Pathological Process =def. – A bodily process that is a manifestation of a disorder and is clinically abnormal.

  • Disease =def. – A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.


Influenza infectious

But the disorder also induces normal physiological processes (immune response) that can results in the elimination of the disorder (transient disease course).

Influenza - infectious

  • Symptoms & Signs

    • used_in

  • Interpretive process

    • produces

  • Hypothesis - rule out influenza

    • suggests

  • Laboratory tests

    • produces

  • Test results - elevated serum antibody titers

    • used_in

  • Interpretive process

    • produces

  • Result - diagnosis that patient X has a disorder that bears the disease flu

  • Etiological process - infection of airway epithelial cells with influenza virus

    • produces

  • Disorder - viable cells with influenza virus

    • bears

  • Disposition (disease) - flu

    • realized_in

  • Pathological process - acute inflammation

    • produces

  • Abnormal bodily features

    • recognized_as

  • Symptoms - weakness, dizziness

  • Signs - fever


Huntington s disease genetic

Huntington’s Disease - genetic

  • Symptoms & Signs

    • used_in

  • Interpretive process

    • produces

  • Hypothesis - rule out Huntington’s

    • suggests

  • Laboratory tests

    • produces

  • Test results - molecular detection of the HTT gene with >39CAG repeats

    • used_in

  • Interpretive process

    • produces

  • Result - diagnosis that patient X has a disorder that bears the disease Huntington’s disease

  • Etiological process - inheritance of >39 CAG repeats in the HTT gene

    • produces

  • Disorder - chromosome 4 with abnormal mHTT

    • bears

  • Disposition (disease) - Huntington’s disease

    • realized_in

  • Pathological process - accumulation of mHTT protein fragments, abnormal transcription regulation, neuronal cell death in striatum

    • produces

  • Abnormal bodily features

    • recognized_as

  • Symptoms - anxiety, depression

  • Signs - difficulties in speaking and swallowing


Hnpcc genetic pre disposition

HNPCC - genetic pre-disposition

  • Etiological process - inheritance of a mutant mismatch repair gene

    • produces

  • Disorder - chromosome 3 with abnormal hMLH1

    • bears

  • Disposition (disease) - Lynch syndrome

    • realized_in

  • Pathological process - abnormal repair of DNA mismatches

    • produces

  • Disorder - mutations in proto-oncogenes and tumor suppressor genes with microsatellite repeats (e.g. TGF-beta R2)

    • bears

  • Disposition (disease) - non-polyposis colon cancer

    • realized in

  • Symptoms (including pain)


Dispositions and predispositions

Dispositions and Predispositions

  • All diseases are dispositions; not all dispositions are diseases.

  • A predisposition is a disposition to acquire a disposition.

  • Predisposition to Disease of Type X =def.– A disposition in an organism that constitutes an increased risk of the organism’s subsequently developing the disease X.

  • HNPCC is caused by a

    • disorder (mutation) in a DNA mismatch repair gene that

    • disposes to the acquisition of additional mutations from defective DNA repair processes, and thus is a

    • predisposition to the development of colon cancer.


Cirrhosis environmental exposure

Cirrhosis - environmental exposure

  • Symptoms & Signs

    • used_in

  • Interpretive process

    • produces

  • Hypothesis - rule out cirrhosis

    • suggests

  • Laboratory tests

    • produces

  • Test results - elevated liver enzymes in serum

    • used_in

  • Interpretive process

    • produces

  • Result - diagnosis that patient X has a disorder that bears the disease cirrhosis

  • Etiological process - phenobarbitol-induced hepatic cell death

    • produces

  • Disorder - necrotic liver

    • bears

  • Disposition (disease) - cirrhosis

    • realized_in

  • Pathological process - abnormal tissue repair with cell proliferation and fibrosis that exceed a certain threshold; hypoxia-induced cell death

    • produces

  • Abnormal bodily features

    • recognized_as

  • Symptoms - fatigue, anorexia

  • Signs - jaundice, splenomegaly


Systemic arterial hypertension

Systemic arterial hypertension

  • Symptoms & Signs

    • used_in

  • Interpretive process

    • produces

  • Hypothesis - rule out hypertension

    • suggests

  • Laboratory tests

    • produces

  • Test results -

    • used_in

  • Interpretive process

    • produces

  • Result - diagnosis that patient X has a disorder that bears the disease hypertension

  • Etiological process – abnormal reabsorption of NaCl by the kidney

    • produces

  • Disorder – abnormally large scattered molecular aggregate of salt in the blood

    • bears

  • Disposition (disease) - hypertension

    • realized_in

  • Pathological process – exertion of abnormal pressure against arterial wall

    • produces

  • Abnormal bodily features

    • recognized_as

  • Symptoms -

  • Signs – elevated blood pressure


Type 2 diabetes mellitus

Type 2 Diabetes Mellitus

  • Symptoms & Signs

    • used_in

  • Interpretive process

    • produces

  • Hypothesis - rule out diabetes mellitus

    • suggests

  • Laboratory tests – fasting serum blood glucose, oral glucose challenge test, and/or blood hemoglobin A1c

    • produces

  • Test results -

    • used_in

  • Interpretive process

    • produces

  • Result - diagnosis that patient X has a disorder that bears the disease type 2 diabetes mellitus

  • Etiological process –

    • produces

  • Disorder – abnormal pancreatic beta cells and abnormal muscle/fat cells

    • bears

  • Disposition (disease) – diabetes mellitus

    • realized_in

  • Pathological processes – diminished insulin production , diminished muscle/fat uptake of glucose

    • produces

  • Abnormal bodily features

    • recognized_as

  • Symptoms – polydipsia, polyuria, polyphagia, blurred vision

  • Signs – elevated blood glucose and hemoglobin A1c


Type 1 hypersensitivity to penicillin

Type 1 hypersensitivity to penicillin

  • Symptoms & Signs

    • used_in

  • Interpretive process

    • produces

  • Hypothesis -

    • suggests

  • Laboratory tests –

    • produces

  • Test results – occasionally, skin testing

    • used_in

  • Interpretive process

    • produces

  • Result - diagnosis that patient X has a disorder that bears the disease type 1 hypersensitivity to penicillin

  • Etiological process – sensitizing of mast cells and basophils during exposure to penicillin-class substance

    • produces

  • Disorder – mast cells and basophils with epitope-specific IgE bound to Fc epsilon receptor I

    • bears

  • Disposition (disease) – type I hypersensitivity

    • realized_in

  • Pathological process – type I hypersensitivity reaction

    • produces

  • Abnormal bodily features

    • recognized_as

  • Symptoms – pruritis, shortness of breath

  • Signs – rash, urticaria, anaphylaxis


Next steps in ogms

Next steps in OGMS

  • classification of distinct types of disease courses for instances of each disease type

    • in different typical environments

    • with and without treatment

    • with treatment plan that is or is not realized by the patient

    • where the disease exists in combination with other diseases


Next steps in ogms1

Next steps in OGMS

  • modify the Big Picture to take account of differences between primary care and specialist care


The big picture1

The Big Picture


Definitions clinical evaluation terms

Definitions - Clinical Evaluation Terms

  • Sign =def. – A bodily feature of a patient that is observed in a physical examination and is deemed by the clinician to be of clinical significance. (Objectively observable features)

  • Symptom =def. – An experienced bodily feature of a patient that is observed by and observable only by the patient and is of the type that can be hypothesized by a patient to be a realization of a disease. (A restricted family of phenomena including pain, nausea, anger, drowsiness, which are of their nature experienced in the first person)

    Symptoms are subjective. But this does not mean that there is no objective fact of the matter whether a given symptom exists


Definition etiology

Definition: Etiology

  • Etiological Process =def. – A process in an organism that leads to a subsequent disorder.

  • Example: toxic chemical exposure resulting in a mutation in the genomic DNA of a cell; infection of a human with a pathogenic virus; inheritance of two defective copies of a metabolic gene

  • The etiological process creates the physical basis of that disposition to pathological processes which is the disease.


Definitions diagnosis

Definitions - Diagnosis

  • Clinical Picture =def. – A representation of a clinical phenotype that is inferred from the combination of laboratory, image and clinical findings about a given patient.

  • Diagnosis =def. – A conclusion of an interpretive process that has as input a clinical picture of a given patient and as output an assertion to the effect that the patient has a disease of such and such a type.


Definitions qualities

Definitions - Qualities

  • Manifestation of a Disease =def. – A bodily feature of a patient that is (a) a deviation from clinical normality that exists in virtue of the realization of a disease and (b) is observable.

    • Observability includes observable through elicitation of response or through the use of special instruments.

  • Preclinical Manifestation of a Disease =def. – A manifestation of a disease that exists prior to its becoming detectable in a clinical history taking or physical examination.

  • Clinical Manifestation of a Disease =def. – A manifestation of a disease that is detectable in a clinical history taking or physical examination.

  • Phenotype =def. – A (combination of) bodily feature(s) of an organism determined by the interaction of its genetic make-up and environment.

  • Clinical Phenotype =def. – A clinically abnormal phenotype.


Towards an ontological treatment of disease and diagnosis

  • For an ontology to succeed,

  • potential users should be incentivized to use it,

  • it should be populated using the terms that they need and using definitions that conform to their understanding of these terms

  • it should be easily correctable in light of new research discoveries

  • it should enable the data annotated in its terms to be easily integrated with legacy data from related fields

  • it should be easily extendable to new kinds of data.

http://ontology.buffalo.edu/smith


Towards an ontological treatment of disease and diagnosis

A new kind of Electronic Health Recordresting on the use of the same (public domain) ontologies in mapping proprietary EHR vocabularies to yield patient data annotated in consistent ways that support

integrated care and continuity of care

comparison and integration for diagnosis and meta-analysis

secondary uses for research


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