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The Philosophome: An Exercise in the Ontology of the Humanities

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Information about The Philosophome: An Exercise in the Ontology of the Humanities
Education

Published on February 16, 2014

Author: BarrySmith3

Source: slideshare.net

Description

Presentation at the opening of the Humanomics Research Centre at the University of Copenhagen, 7 February 2014
For background links see: http://philosophome.org/
We describe the methodology of omics disciplines in biology, and consider how analogous methods might be applied in humanities disciplines, focusing specifically on philosophy. We conclude by outlining a possible strategy for a research center in humanomics, identifying possible sources of data in the philosophical domain.
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The Philosophome Barry Smith

Why omics?

Old biology data (cell division) 3

New biology data MKVSDRRKFEKANFDEFESALNNKNDLVHCPSITLFESIPTEVRSF YEDEKSGLIKVVKFRTGAMDRKRSFEKVVISVMVGKNVKKFLTFV EDEPDFQGGPISKYLIPKKINLMVYTLFQVHTLKFNRKDYDTLSLF YLNRGYYNELSFRVLERCHEIASARPNDSSTMRTFTDFVSGAPIV RSLQKSTIRKYGYNLAPYMFLLLHVDELSIFSAYQASLPGEKKVDT ERLKRDLCPRKPIEIKYFSQICNDMMNKKDRLGDILHIILRACALNF GAGPRGGAGDEEDRSITNEEPIIPSVDEHGLKVCKLRSPNTPRRL RKTLDAVKALLVSSCACTARDLDIFDDNNGVAMWKWIKILYHEVA QETTLKDSYRITLVPSSDGISLLAFAGPQRNVYVDDTTRRIQLYTD YNKNGSSEPRLKTLDGLTSDYVFYFVTVLRQMQICALGNSYDAFN HDPWMDVVGFEDPNQVTNRDISRIVLYSYMFLNTAKGCLVEYAT FRQYMRELPKNAPQKLNFREMRQGLIALGRHCVGSRFETDLYES ATSELMANHSVQTGRNIYGVDFSLTSVSGTTATLLQERASERWIQ WLGLESDYHCSFSSTRNAEDVDISRIVLYSYMFLNTAKGCLVEYA TFRQYMRELPKNAPQKLNFREMRQGLIALGRHCVGSRFETDLYE 4 SATSELMANHSVQTGRNIYGVDFSLTSVSGTTATLLQERASERWI

How to do biology across the genome? MKVSDRRKFEKANFDEFESALNNKNDLVHCPSITLFESIPTEVRSFYEDEKSGLIKVVKFRTGAMDRKRSFEKVVIS VMVGKNVKKFLTFVEDEPDFQGGPISKYLIPKKINLMVYTLFQVHTLKFNRKDYDTLSLFYLNRGYYNELSFRVLER CHEIASARPNDSSTMRTFTDFVSGAPIVRSLQKSTIRKYGYNLAPYMFLLLHVDELSIFSAYQASLPGEKKVDTERL KRDLCPRKPIEIKYFSQICNDMMNKKDRLGDILHIILRACALNFGAGPRGGAGDEEDRSITNEEPIIPSVDEHGLKVC KLRSPNTPRRLRKTLDAVKALLVSSCACTARDLDIFDDNNGVAMWKWIKILYHEVAQETTLKDSYRITLVPSSDGIS LLAFAGPQRNVYVDDTTRRIQLYTDYNKNGSSEPRLKTLDGLTSDYVFYFVTVLRQMQICALGNSYDAFNHDPWM DVVGFEDPNQVTNRDISRIVLYSYMFLNTAKGCLVEYATFRQYMRELPKNAPQKLNFREMRQGLIALGRHCVGSR FETDLYESATSELMANHSVQTGRNIYGVDFSLTSVSGTTATLLQERASERWIQWLGLESDYHCSFSSTRNAEDVM KVSDRRKFEKANFDEFESALNNKNDLVHCPSITLFESIPTEVRSFYEDEKSGLIKVVKFRTGAMDRKRSFEKVVISV MVGKNVKKFLTFVEDEPDFQGGPISKYLIPKKINLMVYTLFQVHTLKFNRKDYDTLSLFYLNRGYYNELSFRVLERC HEIASARPNDSSTMRTFTDFVSGAPIVRSLQKSTIRKYGYNLAPYMFLLLHVDELSIFSAYQASLPGEKKVDTERLK RDLCPRKPIEIKYFSQICNDMMNKKDRLGDILHIILRACALNFGAGPRGGAGDEEDRSITNEEPIIPSVDEHGLKVCK LRSPNTPRRLRKTLDAVKALLVSSCACTARDLDIFDDNNGVAMWKWIKILYHEVAQETTLKDSYRITLVPSSDGISLL AFAGPQRNVYVDDTTRRIQLYTDYNKNGSSEPRLKTLDGLTSDYVFYFVTVLRQMQICALGNSYDAFNHDPWMD VVGFEDPNQVTNRDISRIVLYSYMFLNTAKGCLVEYATFRQYMRELPKNAPQKLNFREMRQGLIALGRHCVGSRF ETDLYESATSELMANHSVQTGRNIYGVDFSLTSVSGTTATLLQERASERWIQWLGLESDYHCSFSSTRNAEDVMK VSDRRKFEKANFDEFESALNNKNDLVHCPSITLFESIPTEVRSFYEDEKSGLIKVVKFRTGAMDRKRSFEKVVISVM VGKNVKKFLTFVEDEPDFQGGPISKYLIPKKINLMVYTLFQVHTLKFNRKDYDTLSLFYLNRGYYNELSFRVLERCH EIASARPNDSSTMRTFTDFVSGAPIVRSLQKSTIRKYGYNLAPYMFLLLHVDELSIFSAYQASLPGEKKVDTERLKR DLCPRKPIEIKYFSQICNDMMNKKDRLGDILHIILRACALNFGAGPRGGAGDEEDRSITNEEPIIPSVDEHGLKVCKL RSPNTPRRLRKTLDAVKALLVSSCACTARDLDIFDDNNGVAMWKWIKILYHEVAQETTLKDSYRITLVPSSDGISLL AFAGPQRNVYVDDTTRRIQLYTDYNKNGSSEPRLKTLDGLTSDYVFYFVTVLRQMQICALGNSYDAFNHDPWMD VVGFEDPNQVTNRDISRIVLYSYMFLNTAKGCLVEYATFRQYMRELPKNAPQKLNFREMRQGLIALGRHCVGSRF ETDLYESATSELMANHSVQTGRNIYGVDFSLTSVSGTTATLLQERASERWIQWLGLESDYHCSFSSTRNAEDVMK VSDRRKFEKANFDEFESALNNKNDLVHCPSITLFESIPTEVRSFYEDEKSGLIKVVKFRTGAMDRKRSFEKVVISVM VGKNVKKFLTFVEDEPDFQGGPISKYLIPKKINLMVYTLFQVHTLKFNRKDYDTLSLFYLNRGYYNELSFRVLERCH5 EIASARPNDSSTMRTFTDFVSGAPIVRSLQKSTIRKYGYNLAPYMFLLLHVDELSIFSAYQASLPGEKKVDTERLKR

how to link the kinds of phenomena represented here 6

or here 7

or here 8

MKVSDRRKFEKANFDEFESALNNKNDLVHCPSITLFESIPTEVRSFYEDEKSGLIKVVKFRTGAMDRK RSFEKVVISVMVGKNVKKFLTFVEDEPDFQGGPIPSKYLIPKKINLMVYTLFQVHTLKFNRKDYDTLSL FYLNRGYYNELSFRVLERCHEIASARPNDSSTMRTFTDFVSGAPIVRSLQKSTIRKYGYNLAPYMFLLL HVDELSIFSAYQASLPGEKKVDTERLKRDLCPRKPIEIKYFSQICNDMMNKKDRLGDILHIILRACALNF GAGPRGGAGDEEDRSITNEEPIIPSVDEHGLKVCKLRSPNTPRRLRKTLDAVKALLVSSCACTARDLD IFDDNNGVAMWKWIKILYHEVAQETTLKDSYRITLVPSSDGISLLAFAGPQRNVYVDDTTRRIQLYTDY NKNGSSEPRLKTLDGLTSDYVFYFVTVLRQMQICALGNSYDAFNHDPWMDVVGFEDPNQVTNRDIS RIVLYSYMFLNTAKGCLVEYATFRQYMRELPKNAPQKLNFREMRQGLIALGRHCVGSRFETDLYESA TSELMANHSVQTGRNIYGVDSFSLTSVSGTTATLLQERASERWIQWLGLESDYHCSFSSTRNAEDVV AGEAASSNHHQKISRVTRKRPREPKSTNDILVAGQKLFGSSFEFRDLHQLRLCYEIYMADTPSVAVQA PPGYGKTELFHLPLIALASKGDVEYVSFLFVPYTVLLANCMIRLGRRGCLNVAPVRNFIEEGYDGVTDL YVGIYDDLASTNFTDRIAAWENIVECTFRTNNVKLGYLIVDEFHNFETEVYRQSQFGGITNLDFDAFEK AIFLSGTAPEAVADAALQRIGLTGLAKKSMDINELKRSEDLSRGLSSYPTRMFNLIKEKSEVPLGHVHKI RKKVESQPEEALKLLLALFESEPESKAIVVASTTNEVEELACSWRKYFRVVWIHGKLGAAEKVSRTKE FVTDGSMQVLIGTKLVTEGIDIKQLMMVIMLDNRLNIIELIQGVGRLRDGGLCYLLSRKNSWAARNRKG ELPPKEGCITEQVREFYGLESKKGKKGQHVGCCGSRTDLSADTVELIERMDRLAEKQATASMSIVAL PSSFQESNSSDRYRKYCSSDEDSNTCIHGSANASTNASTNAITTASTNVRTNATTNASTNATTNASTN ASTNATTNASTNATTNSSTNATTTASTNVRTSATTTASINVRTSATTTESTNSSTNATTTESTNSSTNA TTTESTNSNTSATTTASINVRTSATTTESTNSSTSATTTASINVRTSATTTKSINSSTNATTTESTNSNT NATTTESTNSSTNATTTESTNSSTNATTTESTNSNTSAATTESTNSNTSATTTESTNASAKEDANKDG NAEDNRFHPVTDINKESYKRKGSQMVLLERKKLKAQFPNTSENMNVLQFLGFRSDEIKHLFLYGIDIYF CPEGVFTQYGLCKGCQKMFELCVCWAGQKVSYRRIAWEALAVERMLRNDEEYKEYLEDIEPYHGDP VGYLKYFSVKRREIYSQIQRNYAWYLAITRRRETISVLDSTRGKQGSQVFRMSGRQIKELYFKVWSNL RESKTEVLQYFLNWDEKKCQEEWEAKDDTVVVEALEKGGVFQRLRSMTSAGLQGPQYVKLQFSRH HRQLRSRYELSLGMHLRDQIALGVTPSKVPHWTAFLSMLIGLFYNKTFRQKLEYLLEQISEVWLLPHW LDLANVEVLAADDTRVPLYMLMVAVHKELDSDDVPDGRFDILLCRDSSREVGELIGLFYNKTFRQKLE 9 YLLEQISEVWLLPHWLDLANVEVLAADDTRVPLYMLMVAVHKELDSDDVPDGRFDILLCRDSSREVG ELIGLFYNKTFRQKLEYLLEQISEVWLLPHWLDLANVEVLAADDTRVPLYMLMVAVHKELDSDDVPDG to this?

or this? 10

or this? 11

answer: by tagging data with terms from a controlled vocabulary such as the Gene Ontology GO: age-dependent behavioral decline GO: sphingolipid transporter activity GO: Holliday junction helicase complex 12

For example by tagging sequence data MKVSDRRKFEKANFDEFESALNNKNDLVHCPSITLFESIPTEVRSFYEDEKSGLIKVVKFRTGAMDRKRSFEKVVIS VMVGKNVKKFLTFVEDEPDFQGGPIPSKYLIPKKINLMVYTLFQVHTLKFNRKDYDTLSLFYLNRGYYNELSFRVLE RCHEIASARPNDSSTMRTFTDFVSGAPIVRSLQKSTIRKYGYNLAPYMFLLLHVDELSIFSAYQASLPGEKKVDTER LKRDLCPRKPIEIKYFSQICNDMMNKKDRLGDILHIILRACALNFGAGPRGGAGDEEDRSITNEEPIIPSVDEHGLKV CKLRSPNTPRRLRKTLDAVKALLVSSCACTARDLDIFDDNNGVAMWKWIKILYHEVAQETTLKDSYRITLVPSSDGI SLLAFAGPQRNVYVDDTTRRIQLYTDYNKNGSSEPRLKTLDGLTSDYVFYFVTVLRQMQICALGNSYDAFNHDPW MDVVGFEDPNQVTNRDISRIVLYSYMFLNTAKGCLVEYATFRQYMRELPKNAPQKLNFREMRQGLIALGRHCVGS RFETDLYESATSELMANHSVQTGRNIYGVDSFSLTSVSGTTATLLQERASERWIQWLGLESDYHCSFSSTRNAED VVAGEAASSNHHQKISRVTRKRPREPKSTNDILVAGQKLFGSSFEFRDLHQLRLCYEIYMADTPSVAVQAPPGYG KTELFHLPLIALASKGDVEYVSFLFVPYTVLLANCMIRLGRRGCLNVAPVRNFIEEGYDGVTDLYVGIYDDLASTNFT DRIAAWENIVECTFRTNNVKLGYLIVDEFHNFETEVYRQSQFGGITNLDFDAFEKAIFLSGTAPEAVADAALQRIG age-dependent behavioral decline LTGLAKKSMDINELKRSEDLSRGLSSYPTRMFNLIKEKSEVPLGHVHKIRKKVESQPEEALKLL LALFESEPESKAIVVASTTNEVEELACSWRKYFRVVWIHGKLGAAEKVSRTKEFVTDGSMQVLI GTKLVTEGIDIKQLMMVIMLDNRLNIIELIQGVGRLRDGGLCYLLSRKNSWAARNRKGELPPKEGCITE QVREFYGLESKKGKKGQHVGCCGSRTDLSADTVELIERMDRLAEKQATASMSIVALPSSFQESNSSDRYRKYCS SDEDSNTCIHGSANASTNASTNAITTASTNVRTNATTNASTNATTNASTNASTNATTNASTNATTNSSTNATTTAST NVRTSATTTASINVRTSATTTESTNSSTNATTTESTNSSTNATTTESTNSNTSATTTASINVRTSATTTESTNSSTSA TTTASINVRTSATTTKSINSSTNATTTESTNSNTNATTTESTNSSTNATTTESTNSSTNATTTESTNSNTSAATTEST NSNTSATTTESTNASAKEDANKDGNAEDNRFHPVTDINKESYKRKGSQMVLLERKKLKAQFPNTSENMNVLQFLG FRSDEIKHLFLYGIDIYFCPEGVFTQYGLCKGCQKMFELCVCWAGQKVSYRRIAWEALAVERMLRNDEEYKEYLE DIEPYHGDPVGYLKYFSVKRREIYSQIQRNYAWYLAITRRRETISVLDSTRGKQGSQVFRMSGRQIKELYFKVWSN LRESKTEVLQYFLNWDEKKCQEEWEAKDDTVVVEALEKGGVFQRLRSMTSAGLQGPQYVKLQFSRHHRQLRSR YELSLGMHLRDQIALGVTPSKVPHWTAFLSMLIGLFYNKTFRQKLEYLLEQISEVWLLPHWLDLANVEVLAADDTR VPLYMLMVAVHKELDSDDVPDGRFDILLCRDSSREVGELIGLFYNKTFRQKLEYLLEQISEVWLLPHWLDLANVEVL AADDTRVPLYMLMVAVHKELDSDDVPDGRFDILLCRDSSREVGELIGLFYNKTFRQKLEYLLEQISEVWLLPHWLD LANVEVLAADDTRVPLYMLMVAVHKELDSDDVPDGRFDILLCRDSSREVGE 13

tagging allows virtual integration of heterogeneous databases GlyProt MouseEcotope sphingolipid transporter activity DiabetInGene GluChem 14

fosters discoverability of information in heterogeneous databases GlyProt MouseEcotope Holliday junction helicase complex DiabetInGene GluChem 15

Figure 3. tagging of literature RB Reis, GS Ribeiro, RDM Felzemburgh, et al., Impact of Environment and Social Gradient n Leptospira Infection in Urban Slums 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.1000361 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 18

19

RELATION TO TIME CONTINUANT INDEPENDENT OCCURRENT DEPENDENT GRANULARITY ORGAN AND ORGANISM Organism (NCBI Taxonomy) CELL AND CELLULAR COMPONENT Cell (CL) MOLECULE Anatomical Organ Entity Function (FMA, (FMP, CPRO) Phenotypic CARO) Quality (PaTO) Cellular Cellular Component Function (FMA, GO) (GO) Molecule (ChEBI, SO, RnaO, PrO) Molecular Function (GO) Biological Process (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 Ontology Actionable Intelligence Retrieval System (AIRS) Analysis Ontology (CAO) Bank Ontology Beta Cell Genomics Application Ontology (BCGO) BioAssay Ontology Bioinformatics Web Service Ontology Biological Collections Ontology (BCO) Cell Line Ontology (CLO) Cell Ontology Chemical Entities of Biological Interest (ChEBI) CHRONIOUS Ontology Suite Clusters of Orthologous Groups (COG) Cognitive Paradigm Ontology Common Anatomy Reference Ontology (CARO): anatomical structures in all organisms Comunication Standards Ontology (CSO) Conceptual Model Ontology (CMO) Coriell Cell Line Ontology CPR Ontology for the Institute of Medicine's (IOM) ComputerBased Patient Record Ontology Drug Interaction Ontology (DIO): ontology-driven inferences of possible drug-drug Interactions Drug Ontology (DrOn) Drug-drug Interaction Ontology (DINTO) Dynamic Earth Sciences Ontologies: Process and Event Ontologies Emotion Ontology (EMO) Environment Ontology: (ENVO) Evolution Ontology (EO) Experimental Factor Ontology (EFO) Exposé: An Ontology for Data Mining Experiments Financial Report Ontology Flybase 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 Ontology Information Artifact Ontology (IAO) Interdisciplinary Prostate Ontology Project (IPOP) Lipid OntologyIEO) 21/`

At the interface between biomedical omics and humanomics The Emotion Ontology Barry Smith and Janna Hastings* *Swiss Centre for Affective Sciences, University of Geneva, Switzerland and Cheminformatics and Metabolism Team, European Bioinformatics Institute

Many kinds of data emotional functioning, regulation, expression, and physiological markers neuroimaging chemistry (alcohol, …) affective disorders such as bipolar, depression and schizoaffective disorder emotions in organizational behavior, politics … emotions in the literature, drama, dance, … Sunday, February 16, 2014 23

http://bioportal.bioontology.org/ontologies/1666 Sunday, February 16, 2014 The Emotion Ontology 24

Types of feeling in the Emotion Ontology 25

Types of Physiological Response to Emotion 26

Adam Smith 27

Werner Ceusters 28

a “half cut” in Irish Sean-nós dancing 29

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 30

Discoverability How to find –choreography, –dress patterns, –music scores, –descriptions from the social pages relating to the 17th-century English quadrille 31

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 … 32/

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. 33

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 34/

What is the Philosophome? 35/

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 … 36

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 37 and counterarguments, evidence …

The Philosophy Family Tree An academic genealogy of philosophers Only one type of link: is_Doktorvater_of • as wiki • as indented list • as linked graph The largest (and longest) chain of links begins with Leibniz (plus orphans such as Plato) 140,000 entries From 1930 onwards, overwhelmingly Danish Anglo-Saxon 38/

wiki http://philosophyfamilytree.wikispaces.com 39/

as indented list http://ontology.buffalo.edu/philosophome 40/

41/

as linked graph http://ontology.buffalo.edu/philosophome 42

43

44/

45/

46/

47/

Other contributions to the Philosophome • • • • • Randall Collins, The Sociology of Philosophies Holenstein’s Philosophie-Atlas Philosophy Ideas PhilPapers Harzing’s Publish or Perish 48/

49/

50

51/

52/

53/

Continental Drift of Analytic Philosophy

http://philosophyideas.com/ 55

16,216 ideas 56/

pi http://philpapers.org/ 57/

Harzing’s Publish or Perish http://www.harzing.com/ (based on Google scholar) find me all the literature in which Stjernfelt, Copenhagen and the devil are simultaneously mentioned 58

59

Harzing’s Publish or Perish who is the most highly cited philosopher in history? 60

61

62

even all this stuff will be compiled into the Philosophome

The Philosophome needs an ontology 64/

65

philosopher instance_of 66

67

Philonto: subtypes of philosopher 68

A modest proposal for a Humanomics Research Centre 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 69

A modest proposal for a Humanomics Research Centre 4. test the value of such tagging in promoting discoverability of • data • literature • persons (including precursors, potential collaborators) • funders 70

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