Literature Mapping with PubAtlas -- extending PubMed

with a `BLASTing interface’D Stott Parker1, WW Chu1, FW Sabb3, AW Toga2, RM Bilder31UCLA Computer Science Dept, 2Laboratory of Neuroimaging, 3Dept of Psychiatry & Biobehavioral Sciences

Hypothesis Web ProjectNIH RL1LM009833

PubAtlas is a“PubMed BLAST-query”service for two term sets/lexica

PubAtlas Literature Map

result: contingency table for all queries (X AND Y) where X,Y are terms in the two lexica

www.pubatlas.org

PubAtlas Lexica:• term: definition pairs Term Name : PubMed Query• optional hierarchical structure

Lexicon as:• concept base • ontology• user-defined term hierarchy (personalized MeSH hierarchy)• domain-specific query language

Lexica

Concept BLASTing

Lexicon1 = X hierarchy

Literature Map: (X AND Y)

association table

Lexicon2 = Y hierarchy

MEDLINE / PubMed as a bioscience association base

PubAtlas

`Concept BLASTing’ seeks useful associations, much like microarray analysis

Previous Work -- as an example

AliBaba: "AliBaba" [TIAB] AND "PubMed" [TIAB]Anne O'Tate: "Anne O'Tate" [TIAB]BioIE: "BioIE" [TIAB]ClusterMed: "ClusterMed" [TIAB]ConceptLink: "ConceptLink" [TIAB]GoPubMed: "GoPubMed" [TIAB]HubMed: "HubMed" [TIAB]PubFocus: "PubFocus" [TIAB]PubGene: "PubGene" [TIAB]PubMatrix: "PubMatrix" [TIAB]PubMed Assistant: "PubMed Assistant" [TIAB]PubNet: "PubNet" [TIAB]PubReMiner: "PubReMiner" [TIAB]Relemed: "Relemed" [TIAB]SLIM: "Muin M" [au] AND "SLIM" [TIAB]VisualNet: "VisualNet" [TIAB] OR "Visual Net" [TIAB]XplorMed: "XplorMed" [TIAB]

graph: "PubMed" [TIAB] AND ("graph" [TIAB] OR "network" [TIAB] OR "diagram" [TIAB])visual: "PubMed" [TIAB] AND ("visual" [TIAB] OR "visualizing" [TIAB] OR "visualization" [TIAB] …)friendly: "PubMed" [TIAB] AND ("friendly" [TIAB] OR "flexible" [TIAB])better interface: "PubMed" [TIAB] AND ("interface" [TIAB] OR "interaction" [TIAB] OR "query" [TIAB]) …)exploration: "PubMed" [TIAB] AND ("exploration" [TIAB] OR "explore" [TIAB] OR "discovery" [TIAB] …)summarization: "PubMed" [TIAB] AND (summariz* [TIAB] OR digest* [TIAB])map: "PubMed" [TIAB] AND ("mapping" [TIAB] OR "map" [TIAB] OR "mapped" [TIAB])extraction: "PubMed" [TIAB] AND (extract* [TIAB] OR identif* [TIAB])relevance: "PubMed" [TIAB] AND ("relevance" [TIAB] OR "ranking" [TIAB] OR "ordering" [TIAB])powerful: "PubMed" [TIAB] AND ("powerful" [TIAB] OR "extended" [TIAB] OR "advanced" [TIAB])

Desirable extension features

previous PubMed extensions

semi-automatedgeneration of areview paper -- but thorough and remaining up-to-date

PubAtlas -- interesting aspects PubAtlas as a tool for concept “BLASTing”

Moving towards shared, user-defined query/concept languages

Visual literature search with concept maps / literature maps

Building on familiar association mining metaphor Extending PubMed with temporal indexing / concept

evolution Real uses: semi-automated reviews, knowledge mgmt, ...

Applications in Phenomics Phenotypes are often naturally represented as queries Promising applications in interdisciplinary collaboration

Knowledge Management

Who at UCLA works on Dopamine Receptors?

Many possibilities for interdisciplinary collaboration

People as ConceptsLori Altshuler: Altshuler Lori [FAU] OR Altshuler LL [AU]Stephen Marder: Marder Stephen [FAU] OR Marder SR [AU]Carrie Bearden: Bearden Carrie [FAU] OR Bearden CE [AU]Ty Cannon: Cannon Tyrone [FAU] OR Cannon TD [AU]Michael Phelps: Phelps Michael [FAU] OR Phelps ME [AU]John Mazziotta: Mazziotta John [FAU] OR Mazziotta J [AU]Paul Thompson: Thompson Paul M [FAU] OR Thompson PM [AU]Arthur Toga: Toga Arthur [FAU] OR Toga A [AU] Roger Woods: Woods Roger [FAU] OR Woods RP [AU] Bob Bilder: Bilder Robert [FAU] OR Bilder RM [AU]Nelson Freimer: Freimer Nelson [FAU] OR Freimer N [AU]...

Map of publications in which people X, Y both occur as authors

Exploring Associations over Time

Extending PubMed with Time

199820002002200420062008

Historical map of interdisciplinary collaboration at UCLA over 10 yrs

Deeper ExplorationVisualization and interaction along with standard mining of association data

For term sets of size M, N, PubAtlas submits M+N PubMed queries

This can scale to hundreds or thousands of terms

Larger Lexica

CNP_peo ple.t erms CNP investigators, ordered alphabe tical ly CNP. terms freque ntly-used terms in the CNP Mem oryMec hanisms.terms freque ntly-used terms: CNP Mem ory Mec hanisms projec t ResponseInhi biti on.t erms freque ntly-used terms: CNP Response Inhibition proje ct CNP_tea ms.terms CNP investigators, ordered by fiel d CNP_groups.terms CNP investigators, ordered by fiel d, with field names ADHD_gen es.terms a l ist of abou t 50 gen es possibly linked wit h ADHD BP_gen es.terms a l ist of abou t 25 gen es possibly linked wit h BP SZ_gen es.terms a l ist of abou t 50 gen es possibly linked wit h SZ CNP_gen es.terms a l ist of abou t 100 gen es possibly linked wit h ADHD/BP/SZ Pub Brain.t erms Pub Brain vocab ulary: 330 anatomica l regio ns of the brain UCLANeuroscie nceFaculty.terms UCLA Neuroscie nc e faculty, ordered alphabe tical ly MeSH_Amines.terms MeSH hierarchy for Amines MeSH_Aza_Compoun ds.terms MeSH hierarchy for Aza Compounds MeSH_Beh avior. terms MeSH hierarchy for Beh avior MeSH_Brain_Anat om ica l_Regions.terms MeSH hierarchy for Brain Regions MeSH_Brain _Diseases.terms MeSH hierarchy for Brain Diseases MeSH_Catecholami nes.terms MeSH hierarchy for Catec holamines MeSH_Cytoskeleto n.terms MeSH hierarchy for Cytoskeleto n MeSH_dopa mine.t erms MeSH dop amine-relate d terms MeSH_Heterocycl ic_Compoun ds_with_3 _rin gs.terms MeSH hierarchy for Heterocycl ic Compounds (3 ring s) MeSH_Heterocycl ic_Compoun ds_with_4 _rin gs.terms MeSH hierarchy for Heterocycl ic Compounds (4 ring s) MeSH_Heterocycl ic_Compoun ds_with_ bridged _rin gs MeSH hierarchy for Heterocycl ic Compounds (bridge d rin gs) MeSH_Hormon es.terms MeSH hierarchy for Hormones MeSH_Ment al_Disorders.terms MeSH hierarchy for Mental Disorders MeSH_Ment al_Processes.terms MeSH hierarchy for Mental Processes MeSH_Metab ol ic_Brain_Diseases.terms MeSH hierarchy for Metabol ic Pathways MeSH_Neural_Pat hways.terms MeSH hierarchy for Neural Pathw ays MeSH_Neurobeh avioral_Manifestatio ns.terms MeSH hierarchy for Neurobeh avioral Manifestations MeSH_ne urobeh avior. terms MeSH hierarchy for neurobeh avior MeSH_Neurodegen erative_Diseases.terms MeSH hierarchy for Neurodegen erative Diseases MeSH_Neurons.terms MeSH hierarchy for Neurons MeSH_Neurotoxicity_Disorders.terms MeSH hierarchy for Neurotoxici ty Disorders MeSH_Neurotransmitt er_Age nts.terms MeSH hierarchy for Neurotransmitter Age nts MeSH_Neurotransmitt er_Recept ors.terms MeSH hierarchy for Neurotransmitter Receptors MeSH_Neurotransmitt ers.terms MeSH hierarchy for Neurotransmitters MeSH_ne urotransmitt er.terms MeSH hierarchy for neurotransmitter MeSH_Neurotransmitt er_Transport_Proteins.terms MeSH hierarchy for Neurotransmitter Transort Proteins MeSH_Personal ity. terms MeSH hierarchy for Personal ity MeSH_Primat es.terms MeSH hierarchy for Primates MeSH_Rode ntia.t erms MeSH hierarchy for Rodentia MeSH_Sleep _Disorders.terms MeSH hierarchy for Slee p MeSH_Su bstance_Related _Disorders.terms MeSH hierarchy for Substance-relate d Disorders

Diverse, complex phenotypes can be represented as queries (predicates)-- denoting the set of all relevant documents

Phenomic Vocabularies as Lexica

PubMed / MEDLINE = central phenomics database

Query Expansion -- for Phenotypes

Queries (like “n-back test”) can be expanded with terms related to their target concept (like working memory), using statistical models to identify better expansions.

Expansion can improve precision and recall of queries that are being used as models of concepts/phenotypes

N-backWisconsin card sorting

Sternberg

Stroopchoice reaction time

…

paced auditory serial addition

("nback" OR “n-back” OR "wisconsin card sorting" OR "sternberg" OR "working memory capacity" OR "stroop" OR "choice reaction time" OR "paced auditory serial addition" OR "pasat" OR "digit span" OR "delayed match to sample")

"nback"

Summary PubAtlas as a tool for concept “BLASTing”

Lexica are concept bases / user-defined query languages PubAtlas constructs concept maps / literature maps Extends PubMed with temporal indexing Multiple features for exploration, visualization Real uses: semi-automated reviews, who is doing what, ... Many interesting directions for further work

Applications in Phenomics Phenotypes are often naturally represented as queries Promising applications in interdisciplinary collaboration

Thank you!