The Philosophome: An Exercise in the Ontology of the Humanities

The Philosophome

Barry Smith

Why omics?

Old biology data (cell division)

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MKVSDRRKFEKANFDEFESALNNKNDLVHCPSITLFESIPTEVRSFYEDEKSGLIKVVKFRTGAMDRKRSFEKVVISVMVGKNVKKFLTFVEDEPDFQGGPISKYLIPKKINLMVYTLFQVHTLKFNRKDYDTLSLFYLNRGYYNELSFRVLERCHEIASARPNDSSTMRTFTDFVSGAPIVRSLQKSTIRKYGYNLAPYMFLLLHVDELSIFSAYQASLPGEKKVDTERLKRDLCPRKPIEIKYFSQICNDMMNKKDRLGDILHIILRACALNFGAGPRGGAGDEEDRSITNEEPIIPSVDEHGLKVCKLRSPNTPRRLRKTLDAVKALLVSSCACTARDLDIFDDNNGVAMWKWIKILYHEVAQETTLKDSYRITLVPSSDGISLLAFAGPQRNVYVDDTTRRIQLYTDYNKNGSSEPRLKTLDGLTSDYVFYFVTVLRQMQICALGNSYDAFNHDPWMDVVGFEDPNQVTNRDISRIVLYSYMFLNTAKGCLVEYATFRQYMRELPKNAPQKLNFREMRQGLIALGRHCVGSRFETDLYESATSELMANHSVQTGRNIYGVDFSLTSVSGTTATLLQERASERWIQWLGLESDYHCSFSSTRNAEDVDISRIVLYSYMFLNTAKGCLVEYATFRQYMRELPKNAPQKLNFREMRQGLIALGRHCVGSRFETDLYESATSELMANHSVQTGRNIYGVDFSLTSVSGTTATLLQERASERWIQWLGLESDYHCSFSSTRNAEDV

New biology data

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How to do biology across the genome?

MKVSDRRKFEKANFDEFESALNNKNDLVHCPSITLFESIPTEVRSFYEDEKSGLIKVVKFRTGAMDRKRSFEKVVISVMVGKNVKKFLTFVEDEPDFQGGPISKYLIPKKINLMVYTLFQVHTLKFNRKDYDTLSLFYLNRGYYNELSFRVLERCHEIASARPNDSSTMRTFTDFVSGAPIVRSLQKSTIRKYGYNLAPYMFLLLHVDELSIFSAYQASLPGEKKVDTERLKRDLCPRKPIEIKYFSQICNDMMNKKDRLGDILHIILRACALNFGAGPRGGAGDEEDRSITNEEPIIPSVDEHGLKVCKLRSPNTPRRLRKTLDAVKALLVSSCACTARDLDIFDDNNGVAMWKWIKILYHEVAQETTLKDSYRITLVPSSDGISLLAFAGPQRNVYVDDTTRRIQLYTDYNKNGSSEPRLKTLDGLTSDYVFYFVTVLRQMQICALGNSYDAFNHDPWMDVVGFEDPNQVTNRDISRIVLYSYMFLNTAKGCLVEYATFRQYMRELPKNAPQKLNFREMRQGLIALGRHCVGSRFETDLYESATSELMANHSVQTGRNIYGVDFSLTSVSGTTATLLQERASERWIQWLGLESDYHCSFSSTRNAEDVMKVSDRRKFEKANFDEFESALNNKNDLVHCPSITLFESIPTEVRSFYEDEKSGLIKVVKFRTGAMDRKRSFEKVVISVMVGKNVKKFLTFVEDEPDFQGGPISKYLIPKKINLMVYTLFQVHTLKFNRKDYDTLSLFYLNRGYYNELSFRVLERCHEIASARPNDSSTMRTFTDFVSGAPIVRSLQKSTIRKYGYNLAPYMFLLLHVDELSIFSAYQASLPGEKKVDTERLKRDLCPRKPIEIKYFSQICNDMMNKKDRLGDILHIILRACALNFGAGPRGGAGDEEDRSITNEEPIIPSVDEHGLKVCKLRSPNTPRRLRKTLDAVKALLVSSCACTARDLDIFDDNNGVAMWKWIKILYHEVAQETTLKDSYRITLVPSSDGISLLAFAGPQRNVYVDDTTRRIQLYTDYNKNGSSEPRLKTLDGLTSDYVFYFVTVLRQMQICALGNSYDAFNHDPWMDVVGFEDPNQVTNRDISRIVLYSYMFLNTAKGCLVEYATFRQYMRELPKNAPQKLNFREMRQGLIALGRHCVGSRFETDLYESATSELMANHSVQTGRNIYGVDFSLTSVSGTTATLLQERASERWIQWLGLESDYHCSFSSTRNAEDVMKVSDRRKFEKANFDEFESALNNKNDLVHCPSITLFESIPTEVRSFYEDEKSGLIKVVKFRTGAMDRKRSFEKVVISVMVGKNVKKFLTFVEDEPDFQGGPISKYLIPKKINLMVYTLFQVHTLKFNRKDYDTLSLFYLNRGYYNELSFRVLERCHEIASARPNDSSTMRTFTDFVSGAPIVRSLQKSTIRKYGYNLAPYMFLLLHVDELSIFSAYQASLPGEKKVDTERLKRDLCPRKPIEIKYFSQICNDMMNKKDRLGDILHIILRACALNFGAGPRGGAGDEEDRSITNEEPIIPSVDEHGLKVCKLRSPNTPRRLRKTLDAVKALLVSSCACTARDLDIFDDNNGVAMWKWIKILYHEVAQETTLKDSYRITLVPSSDGISLLAFAGPQRNVYVDDTTRRIQLYTDYNKNGSSEPRLKTLDGLTSDYVFYFVTVLRQMQICALGNSYDAFNHDPWMDVVGFEDPNQVTNRDISRIVLYSYMFLNTAKGCLVEYATFRQYMRELPKNAPQKLNFREMRQGLIALGRHCVGSRFETDLYESATSELMANHSVQTGRNIYGVDFSLTSVSGTTATLLQERASERWIQWLGLESDYHCSFSSTRNAEDVMKVSDRRKFEKANFDEFESALNNKNDLVHCPSITLFESIPTEVRSFYEDEKSGLIKVVKFRTGAMDRKRSFEKVVISVMVGKNVKKFLTFVEDEPDFQGGPISKYLIPKKINLMVYTLFQVHTLKFNRKDYDTLSLFYLNRGYYNELSFRVLERCHEIASARPNDSSTMRTFTDFVSGAPIVRSLQKSTIRKYGYNLAPYMFLLLHVDELSIFSAYQASLPGEKKVDTERLKRDLCPRKPIEIKYFSQICNDMMNKKDRLGDILHIILRACALNFGAGPRGGAGDEEDRSITNEEPIIPSVDEHGLKVCKLRSPNTPRRLRKTLDAVKALLVSSCACTARDLDIFDDNNGVAMWKWIKILYHEVAQETTLKDSYRITLVPSSDGISLLAFAGPQRNVYVDDTTRRIQLYTDYNKNGSSEPRLKTLDGLTSDYVFYFVTVLRQMQICALGNSYDAFNHDPWMDVVGFEDPNQVTNRDISRIVLYSYMFLNTAKGCLVEYATFRQYMRELPKNAPQKLNFREMRQGLIALGRHCVGSRFETDLYESATSELMANHSVQTGRNIYGVDFSLTSVSGTTATLLQERASERWIQWLGLESDYHCSFSSTRNAEDV

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how to link the kinds of phenomena represented here

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or here

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or here

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MKVSDRRKFEKANFDEFESALNNKNDLVHCPSITLFESIPTEVRSFYEDEKSGLIKVVKFRTGAMDRKRSFEKVVISVMVGKNVKKFLTFVEDEPDFQGGPIPSKYLIPKKINLMVYTLFQVHTLKFNRKDYDTLSLFYLNRGYYNELSFRVLERCHEIASARPNDSSTMRTFTDFVSGAPIVRSLQKSTIRKYGYNLAPYMFLLLHVDELSIFSAYQASLPGEKKVDTERLKRDLCPRKPIEIKYFSQICNDMMNKKDRLGDILHIILRACALNFGAGPRGGAGDEEDRSITNEEPIIPSVDEHGLKVCKLRSPNTPRRLRKTLDAVKALLVSSCACTARDLDIFDDNNGVAMWKWIKILYHEVAQETTLKDSYRITLVPSSDGISLLAFAGPQRNVYVDDTTRRIQLYTDYNKNGSSEPRLKTLDGLTSDYVFYFVTVLRQMQICALGNSYDAFNHDPWMDVVGFEDPNQVTNRDISRIVLYSYMFLNTAKGCLVEYATFRQYMRELPKNAPQKLNFREMRQGLIALGRHCVGSRFETDLYESATSELMANHSVQTGRNIYGVDSFSLTSVSGTTATLLQERASERWIQWLGLESDYHCSFSSTRNAEDVVAGEAASSNHHQKISRVTRKRPREPKSTNDILVAGQKLFGSSFEFRDLHQLRLCYEIYMADTPSVAVQAPPGYGKTELFHLPLIALASKGDVEYVSFLFVPYTVLLANCMIRLGRRGCLNVAPVRNFIEEGYDGVTDLYVGIYDDLASTNFTDRIAAWENIVECTFRTNNVKLGYLIVDEFHNFETEVYRQSQFGGITNLDFDAFEKAIFLSGTAPEAVADAALQRIGLTGLAKKSMDINELKRSEDLSRGLSSYPTRMFNLIKEKSEVPLGHVHKIRKKVESQPEEALKLLLALFESEPESKAIVVASTTNEVEELACSWRKYFRVVWIHGKLGAAEKVSRTKEFVTDGSMQVLIGTKLVTEGIDIKQLMMVIMLDNRLNIIELIQGVGRLRDGGLCYLLSRKNSWAARNRKGELPPKEGCITEQVREFYGLESKKGKKGQHVGCCGSRTDLSADTVELIERMDRLAEKQATASMSIVALPSSFQESNSSDRYRKYCSSDEDSNTCIHGSANASTNASTNAITTASTNVRTNATTNASTNATTNASTNASTNATTNASTNATTNSSTNATTTASTNVRTSATTTASINVRTSATTTESTNSSTNATTTESTNSSTNATTTESTNSNTSATTTASINVRTSATTTESTNSSTSATTTASINVRTSATTTKSINSSTNATTTESTNSNTNATTTESTNSSTNATTTESTNSSTNATTTESTNSNTSAATTESTNSNTSATTTESTNASAKEDANKDGNAEDNRFHPVTDINKESYKRKGSQMVLLERKKLKAQFPNTSENMNVLQFLGFRSDEIKHLFLYGIDIYFCPEGVFTQYGLCKGCQKMFELCVCWAGQKVSYRRIAWEALAVERMLRNDEEYKEYLEDIEPYHGDPVGYLKYFSVKRREIYSQIQRNYAWYLAITRRRETISVLDSTRGKQGSQVFRMSGRQIKELYFKVWSNLRESKTEVLQYFLNWDEKKCQEEWEAKDDTVVVEALEKGGVFQRLRSMTSAGLQGPQYVKLQFSRHHRQLRSRYELSLGMHLRDQIALGVTPSKVPHWTAFLSMLIGLFYNKTFRQKLEYLLEQISEVWLLPHWLDLANVEVLAADDTRVPLYMLMVAVHKELDSDDVPDGRFDILLCRDSSREVGELIGLFYNKTFRQKLEYLLEQISEVWLLPHWLDLANVEVLAADDTRVPLYMLMVAVHKELDSDDVPDGRFDILLCRDSSREVGELIGLFYNKTFRQKLEYLLEQISEVWLLPHWLDLANVEVLAADDTRVPLYMLMVAVHKELDSDDVPDGRFDILLCRDSSREVGE

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to this?

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or this?

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or this?

answer: by tagging data with terms from a controlled vocabulary such as the Gene Ontology

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GO: sphingolipid transporter activity

GO: Holliday junction helicase complex

GO: age-dependent behavioral decline

For example by tagging sequence data

MKVSDRRKFEKANFDEFESALNNKNDLVHCPSITLFESIPTEVRSFYEDEKSGLIKVVKFRTGAMDRKRSFEKVVISVMVGKNVKKFLTFVEDEPDFQGGPIPSKYLIPKKINLMVYTLFQVHTLKFNRKDYDTLSLFYLNRGYYNELSFRVLERCHEIASARPNDSSTMRTFTDFVSGAPIVRSLQKSTIRKYGYNLAPYMFLLLHVDELSIFSAYQASLPGEKKVDTERLKRDLCPRKPIEIKYFSQICNDMMNKKDRLGDILHIILRACALNFGAGPRGGAGDEEDRSITNEEPIIPSVDEHGLKVCKLRSPNTPRRLRKTLDAVKALLVSSCACTARDLDIFDDNNGVAMWKWIKILYHEVAQETTLKDSYRITLVPSSDGISLLAFAGPQRNVYVDDTTRRIQLYTDYNKNGSSEPRLKTLDGLTSDYVFYFVTVLRQMQICALGNSYDAFNHDPWMDVVGFEDPNQVTNRDISRIVLYSYMFLNTAKGCLVEYATFRQYMRELPKNAPQKLNFREMRQGLIALGRHCVGSRFETDLYESATSELMANHSVQTGRNIYGVDSFSLTSVSGTTATLLQERASERWIQWLGLESDYHCSFSSTRNAEDVVAGEAASSNHHQKISRVTRKRPREPKSTNDILVAGQKLFGSSFEFRDLHQLRLCYEIYMADTPSVAVQAPPGYGKTELFHLPLIALASKGDVEYVSFLFVPYTVLLANCMIRLGRRGCLNVAPVRNFIEEGYDGVTDLYVGIYDDLASTNFTDRIAAWENIVECTFRTNNVKLGYLIVDEFHNFETEVYRQSQFGGITNLDFDAFEKAIFLSGTAPEAVADAALQRIGLTGLAKKSMDINELKRSEDLSRGLSSYPTRMFNLIKEKSEVPLGHVHKIRKKVESQPEEALKLLLALFESEPESKAIVVASTTNEVEELACSWRKYFRVVWIHGKLGAAEKVSRTKEFVTDGSMQVLIGTKLVTEGIDIKQLMMVIMLDNRLNIIELIQGVGRLRDGGLCYLLSRKNSWAARNRKGELPPKEGCITEQVREFYGLESKKGKKGQHVGCCGSRTDLSADTVELIERMDRLAEKQATASMSIVALPSSFQESNSSDRYRKYCSSDEDSNTCIHGSANASTNASTNAITTASTNVRTNATTNASTNATTNASTNASTNATTNASTNATTNSSTNATTTASTNVRTSATTTASINVRTSATTTESTNSSTNATTTESTNSSTNATTTESTNSNTSATTTASINVRTSATTTESTNSSTSATTTASINVRTSATTTKSINSSTNATTTESTNSNTNATTTESTNSSTNATTTESTNSSTNATTTESTNSNTSAATTESTNSNTSATTTESTNASAKEDANKDGNAEDNRFHPVTDINKESYKRKGSQMVLLERKKLKAQFPNTSENMNVLQFLGFRSDEIKHLFLYGIDIYFCPEGVFTQYGLCKGCQKMFELCVCWAGQKVSYRRIAWEALAVERMLRNDEEYKEYLEDIEPYHGDPVGYLKYFSVKRREIYSQIQRNYAWYLAITRRRETISVLDSTRGKQGSQVFRMSGRQIKELYFKVWSNLRESKTEVLQYFLNWDEKKCQEEWEAKDDTVVVEALEKGGVFQRLRSMTSAGLQGPQYVKLQFSRHHRQLRSRYELSLGMHLRDQIALGVTPSKVPHWTAFLSMLIGLFYNKTFRQKLEYLLEQISEVWLLPHWLDLANVEVLAADDTRVPLYMLMVAVHKELDSDDVPDGRFDILLCRDSSREVGELIGLFYNKTFRQKLEYLLEQISEVWLLPHWLDLANVEVLAADDTRVPLYMLMVAVHKELDSDDVPDGRFDILLCRDSSREVGELIGLFYNKTFRQKLEYLLEQISEVWLLPHWLDLANVEVLAADDTRVPLYMLMVAVHKELDSDDVPDGRFDILLCRDSSREVGE 13

age-dependent behavioral decline

MouseEcotope GlyProt

DiabetInGene

GluChem

sphingolipid transporter

activity

tagging allows virtual integration of heterogeneous databases

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MouseEcotope GlyProt

DiabetInGene

GluChem

Holliday junction helicase complex

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fosters discoverability of information in heterogeneous databases

Figure 3.

Shotton D, Portwin K, Klyne G, Miles A (2009) Adventures in Semantic Publishing: Exemplar Semantic Enhancements of a Research Article. PLoS Comput Biol 5(4): e1000361. doi:10.1371/journal.pcbi.1000361http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000361

tagging of literature RB Reis, GS Ribeiro, RDM Felzemburgh, et al., Impact of Environ-ment and Social Gradient n Leptospira Infection in Urban Slums

http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000361

coordinated tagging of literature and data

coordinated tagging of literature and data advances

• discoverability • integration• logical reasoning• cross-discipinary collaboration

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RELATION TO TIME

GRANULARITY

CONTINUANT OCCURRENT

INDEPENDENT DEPENDENT

ORGAN ANDORGANISM

Organism(NCBI

Taxonomy)

Anatomical Entity(FMA, CARO)

OrganFunction

(FMP, CPRO) Phenotypic

Quality(PaTO)

Biological Process

(GO)CELL AND CELLULAR

COMPONENT

Cell(CL)

Cellular Compone

nt(FMA, GO)

Cellular Function

(GO)

MOLECULEMolecule

(ChEBI, SO,RnaO, PrO)

Molecular Function(GO)

Molecular Process

(GO)OBO (Open Biomedical Ontology) Foundry proposal

(Gene Ontology in yellow) 20

now many biomedical ontologies developed to coordinate with the OBO Foundry

ACGT Master Ontology (ACGT MO): Alzheimer Disease Ontology (ADO)Adverse Event Ontology (AEO)Adverse Event Reporting Ontology (AERO)AFO Foundational OntologyActionable Intelligence Retrieval System (AIRS)Analysis Ontology (CAO)Bank OntologyBeta Cell Genomics Application Ontology (BCGO)BioAssay OntologyBioinformatics Web Service OntologyBiological Collections Ontology (BCO)Cell Line Ontology (CLO)Cell OntologyChemical Entities of Biological Interest (ChEBI)CHRONIOUS Ontology SuiteClusters of Orthologous Groups (COG)

Cognitive Paradigm OntologyCommon Anatomy Reference Ontology (CARO): anatomical structures in all organismsComunication Standards Ontology (CSO)Conceptual Model Ontology (CMO)Coriell Cell Line OntologyCPR Ontology for the Institute of Medicine's (IOM) Computer-Based Patient Record OntologyDrug Interaction Ontology (DIO): ontology-driven inferences of possible drug-drug InteractionsDrug Ontology (DrOn)Drug-drug Interaction Ontology (DINTO)Dynamic Earth Sciences Ontologies: Process and Event OntologiesEmotion Ontology (EMO)Environment Ontology: (ENVO)Evolution Ontology (EO)

Experimental Factor Ontology (EFO)ExposÃ©: An Ontology for Data Mining ExperimentsFinancial Report OntologyFlybase Drosophila Anatomy Ontology (FBbt)Fission Yeast Phenotype Ontology (FYPO)Foundational Model of Anatomy (FMA): Gastrointestinal Endoscopy Ontology (GGene Regulation Ontology (GRO)Health Data Ontology Trunk (HDOT)Human Interaction Network Ontology (HINO)Infectious Disease OntologyInformation Artifact Ontology (IAO)Interdisciplinary Prostate Ontology Project (IPOP)Lipid OntologyIEO)

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The Emotion Ontology

*Swiss Centre for Affective Sciences, University of Geneva, Switzerland and Cheminformatics and Metabolism Team, European Bioinformatics Institute

Barry Smith and Janna Hastings*

At the interface between biomedical omics and

humanomics

Tuesday, April 11, 2023 23/24

Many kinds of dataemotional functioning, regulation,

expression, and physiological markers neuroimagingchemistry (alcohol, …)affective disorders such as bipolar,

depression and schizoaffective disorderemotions in organizational behavior, politics …emotions in the literature, drama, dance, …

PHILOSOPHY | PSYCHOLOGY | NEUROSCIENCE | PSYCHIATRY | LINGUISTICS

Tuesday, April 11, 202324

http://bioportal.bioontology.org/ontologies/1666

The Emotion Ontology

Types of feeling in the Emotion Ontology

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Types of Physiological Response to Emotion

Adam Smith

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Werner Ceusters

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a “half cut” in Irish Sean-nós dancing

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a short movement of one lower leg crossing the other leg with the foot

pointing outward• part of a mannequin’s step on the catwalk• an epileptic jerk• the kicking of a ball by a soccer player• a signal (“Get out!”) issued in heated

conversation

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Discoverability

How to find –choreography, –dress patterns, –music scores, –descriptions from the social pages

relating to the 17th-century English quadrille

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Answer: build the danceome

= a collection (knowledgebase) of all the digital artifacts (data, literature, images) we have pertaining to dance, including• journalism, fiction, history, …• biographies of dancers, dance impressarios, …• paintings, photographs, vidoes, dress patterns,

museum artifacts …• choreographical scores …

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Convention for the Safeguarding of the Intangible Cultural Heritage (UNESCO 2003)

The earlier “folklore” model supported scholars and institutions in documenting and preserving a record of disappearing traditions. The more recent model aims to sustain a living tradition by supporting the conditions necessary for cultural reproduction.

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At the same time build a Dance Ontology

combine it with a Music Ontology, a Dress Ontology, a Body Movement Ontology …and use the result to annotate the danceome

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What is the Philosophome?

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A collection of data and literature relating to – people– sociology

• schools• movements• places• organizations • surrounding cultural and historical events

– publications, editions– ideas, examples and counterexamples,

arguments and counterarguments, evidence …

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What is the philosophome?A collection of data and literature relating to

–people– sociology

• schools• movements• places• organizations • surrounding cultural and historical events

– publications, editions– ideas, examples and counterexamples, arguments

and counterarguments, evidence …37

The Philosophy Family TreeAn academic genealogy of philosophersOnly one type of link: is_Doktorvater_of• as wiki• as indented list• as linked graphThe largest (and longest) chain of links begins with Leibniz (plus orphans such as Plato)140,000 entriesFrom 1930 onwards, overwhelmingly Danish Anglo-Saxon

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wiki

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http://philosophyfamilytree.wikispaces.com

40/http://ontology.buffalo.edu/philosophome

as indented list

http://ontology.buffalo.edu/philosophome 42

as linked graph

Other contributions to the Philosophome

• Randall Collins, The Sociology of Philosophies• Holenstein’s Philosophie-Atlas• Philosophy Ideas• PhilPapers• Harzing’s Publish or Perish

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Continental Drift of Analytic Philosophy

55http://philosophyideas.com/

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16,216 ideas

pi

57/http://philpapers.org/

Harzing’s Publish or Perish

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http://www.harzing.com/(based on Google scholar)

find me all the literature in which Stjernfelt, Copenhagen and the devil are simultaneously mentioned

http://www.harzing.com/

http://www.harzing.com/

Harzing’s Publish or Perish

who is the most highly cited philosopher in history?

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even all this stuff will be compiled into the Philosophome

The Philosophome needs an ontology

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philosopher

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instance_of

Philonto: subtypes of philosopher

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A modest proposal for a Humanomics Research Centre

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1. adopt the Philosophy Family Tree and extend it, both geographically and ontologically

2. create a suite of coordinated ontologies in philosophy and in neighboring areas of the humanities

3. use these ontologies to curate literature and to tag data about humanities research in Denmark and in the rest of the known universe

A modest proposal for a Humanomics Research Centre

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4. test the value of such tagging in promoting discoverability of• data• literature• persons (including precursors,

potential collaborators)• funders

The Philosophome: An Exercise in the Ontology of the Humanities

Education

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