The Philosophome
Barry Smith
Why omics?
Old biology data (cell division)

3
New biology data

MKVSDRRKFEKANFDEFESALNNKNDLVHCPSITLFESIPTEVRSF
YEDEKSGLIKVVKFRTGAMDRKRSFEKVVISVMVGKNVKKFLTFV
EDEPDFQGGPI...
How to do biology across the genome?
MKVSDRRKFEKANFDEFESALNNKNDLVHCPSITLFESIPTEVRSFYEDEKSGLIKVVKFRTGAMDRKRSFEKVVIS
VMVGKNV...
how to link the kinds of
phenomena represented here

6
or here

7
or here

8
MKVSDRRKFEKANFDEFESALNNKNDLVHCPSITLFESIPTEVRSFYEDEKSGLIKVVKFRTGAMDRK
RSFEKVVISVMVGKNVKKFLTFVEDEPDFQGGPIPSKYLIPKKINLMVYTLFQ...
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 de...
For example by tagging sequence
data
MKVSDRRKFEKANFDEFESALNNKNDLVHCPSITLFESIPTEVRSFYEDEKSGLIKVVKFRTGAMDRKRSFEKVVIS
VMVGKNV...
tagging allows virtual integration of
heterogeneous databases
GlyProt

MouseEcotope
sphingolipid
transporter
activity

Dia...
fosters discoverability of information in
heterogeneous databases
GlyProt

MouseEcotope

Holliday junction
helicase comple...
Figure 3.

tagging of literature
RB Reis, GS Ribeiro, RDM Felzemburgh, et al., Impact of Environment and Social Gradient n...
coordinated tagging of
literature and data
coordinated tagging of literature
and data advances
•
•
•
•

discoverability
integration
logical reasoning
cross-discipina...
19
RELATION
TO TIME

CONTINUANT

INDEPENDENT

OCCURRENT

DEPENDENT

GRANULARITY

ORGAN AND
ORGANISM

Organism
(NCBI
Taxonomy)...
now many biomedical ontologies developed
to coordinate with the OBO Foundry
ACGT Master Ontology (ACGT MO):
Alzheimer Dise...
At the interface between
biomedical omics and
humanomics
The Emotion Ontology
Barry Smith and Janna Hastings*

*Swiss Cent...
Many kinds of data
emotional functioning, regulation,
expression, and physiological markers
neuroimaging
chemistry (alc...
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 ste...
Discoverability
How to find
–choreography,
–dress patterns,
–music scores,
–descriptions from the social pages

relating t...
Answer: build the danceome
= a collection (knowledgebase) of all the digital
artifacts (data, literature, images) we have
...
Convention for the Safeguarding of the
Intangible Cultural Heritage (UNESCO 2003)
The earlier “folklore” model supported s...
At the same time build a Dance
Ontology
combine it with a Music Ontology, a Dress
Ontology, a Body Movement Ontology …
and...
What is the Philosophome?

35/
A collection of data and literature relating to
– people
– sociology
• schools
• movements
• places
• organizations
• surr...
What is the philosophome?
A collection of data and literature relating to

–people
– sociology
•
•
•
•
•

schools
movement...
The Philosophy Family Tree
An academic genealogy of philosophers
Only one type of link: is_Doktorvater_of
• as wiki
• as i...
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...
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
Stjernf...
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 ...
A modest proposal for a
Humanomics Research Centre
4. test the value of such tagging in
promoting discoverability of
• dat...
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The Philosophome: An Exercise in the Ontology of the Humanities

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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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  • http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=116006492sequence of X chromosome in baker’s yeast
  • http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=116006492sequence of X chromosome in baker’s yeast
  • http://ehealthadvice.info/what-is-crohns-disease/
  • http://www.topnews.in/health/why-schizophrenia-patients-may-have-trouble-reading-social-cues-212138
  • http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=116006492
  • BMC Systems BiologyJanuary 2011, 5:17,Open AccessInitial characterization of the human central proteomeThomas R Burkard,
  • http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=116006492
  • Roderic Page: http://iphylo.blogspot.co.uk/2009/04/semantic-publishing-towards-real.html
  • Ontologies are tools widely used in the biomedical sciences for the annotation of high-throughput data, the disambiguation of terminology used in scientific communication, and to enable principled aggregation of disparate data being generated by a variety of methods so as to facilitate complex statistical analyses. With the Emotion Ontology, we are developing such a tool for a wide range of applications within the affective sciences. The deployment and use of the ontology for complex data annotation depends on a consensus within the scientific community as to the nature of the objects of research within the domain and the organisation of these descriptive categories into a formal hierarchy. Logic-based definitions based on Description Logics, the decidable family of fragments of first-order logic that underlies the international standard Web Ontology Language (OWL), allow enhanced computability based on the ontology, bringing benefits to the user such as automatic error detection and consistency checking. In this talk I will give a broad overview of the field of bio-ontologies, both the applications and the underlying technologies, and discuss the preliminary structure of the Emotion Ontology which is currently under development as well as its potential applications.
  • Affective science is the study of emotions and of affective phenomena suchas moods, affects and bodily feelings. It combines the perspectives of many dis-ciplines, such as neuroscience, psychology and philosophy [2]. Emotions have adeep and profound influence on all aspects of human functioning, and altered ordysfunctional emotional responses are implicated in both the etiology and thesymptomology of many pathological conditions. Depression, for example, whichis characterised by abnormally low affect and generally attened emotional re-actions, is one of the fastest-growing public health problems in many countries,corresponding to massive growth in sales of pharmaceuticals (and other sub-stances) which target human aect
  • Essays on philosophical subjects
  • The Philosophome: An Exercise in the Ontology of the Humanities

    1. 1. The Philosophome Barry Smith
    2. 2. Why omics?
    3. 3. Old biology data (cell division) 3
    4. 4. New biology data MKVSDRRKFEKANFDEFESALNNKNDLVHCPSITLFESIPTEVRSF YEDEKSGLIKVVKFRTGAMDRKRSFEKVVISVMVGKNVKKFLTFV EDEPDFQGGPISKYLIPKKINLMVYTLFQVHTLKFNRKDYDTLSLF YLNRGYYNELSFRVLERCHEIASARPNDSSTMRTFTDFVSGAPIV RSLQKSTIRKYGYNLAPYMFLLLHVDELSIFSAYQASLPGEKKVDT ERLKRDLCPRKPIEIKYFSQICNDMMNKKDRLGDILHIILRACALNF GAGPRGGAGDEEDRSITNEEPIIPSVDEHGLKVCKLRSPNTPRRL RKTLDAVKALLVSSCACTARDLDIFDDNNGVAMWKWIKILYHEVA QETTLKDSYRITLVPSSDGISLLAFAGPQRNVYVDDTTRRIQLYTD YNKNGSSEPRLKTLDGLTSDYVFYFVTVLRQMQICALGNSYDAFN HDPWMDVVGFEDPNQVTNRDISRIVLYSYMFLNTAKGCLVEYAT FRQYMRELPKNAPQKLNFREMRQGLIALGRHCVGSRFETDLYES ATSELMANHSVQTGRNIYGVDFSLTSVSGTTATLLQERASERWIQ WLGLESDYHCSFSSTRNAEDVDISRIVLYSYMFLNTAKGCLVEYA TFRQYMRELPKNAPQKLNFREMRQGLIALGRHCVGSRFETDLYE 4 SATSELMANHSVQTGRNIYGVDFSLTSVSGTTATLLQERASERWI
    5. 5. 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
    6. 6. how to link the kinds of phenomena represented here 6
    7. 7. or here 7
    8. 8. or here 8
    9. 9. 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?
    10. 10. or this? 10
    11. 11. or this? 11
    12. 12. 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
    13. 13. 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
    14. 14. tagging allows virtual integration of heterogeneous databases GlyProt MouseEcotope sphingolipid transporter activity DiabetInGene GluChem 14
    15. 15. fosters discoverability of information in heterogeneous databases GlyProt MouseEcotope Holliday junction helicase complex DiabetInGene GluChem 15
    16. 16. 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
    17. 17. coordinated tagging of literature and data
    18. 18. coordinated tagging of literature and data advances • • • • discoverability integration logical reasoning cross-discipinary collaboration 18
    19. 19. 19
    20. 20. 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
    21. 21. 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/`
    22. 22. 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
    23. 23. 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
    24. 24. http://bioportal.bioontology.org/ontologies/1666 Sunday, February 16, 2014 The Emotion Ontology 24
    25. 25. Types of feeling in the Emotion Ontology 25
    26. 26. Types of Physiological Response to Emotion 26
    27. 27. Adam Smith 27
    28. 28. Werner Ceusters 28
    29. 29. a “half cut” in Irish Sean-nós dancing 29
    30. 30. 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
    31. 31. Discoverability How to find –choreography, –dress patterns, –music scores, –descriptions from the social pages relating to the 17th-century English quadrille 31
    32. 32. 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/
    33. 33. 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
    34. 34. 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/
    35. 35. What is the Philosophome? 35/
    36. 36. 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
    37. 37. 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 …
    38. 38. 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/
    39. 39. wiki http://philosophyfamilytree.wikispaces.com 39/
    40. 40. as indented list http://ontology.buffalo.edu/philosophome 40/
    41. 41. 41/
    42. 42. as linked graph http://ontology.buffalo.edu/philosophome 42
    43. 43. 43
    44. 44. 44/
    45. 45. 45/
    46. 46. 46/
    47. 47. 47/
    48. 48. 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. 49. 49/
    50. 50. 50
    51. 51. 51/
    52. 52. 52/
    53. 53. 53/
    54. 54. Continental Drift of Analytic Philosophy
    55. 55. http://philosophyideas.com/ 55
    56. 56. 16,216 ideas 56/
    57. 57. pi http://philpapers.org/ 57/
    58. 58. 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. 59. 59
    60. 60. Harzing’s Publish or Perish who is the most highly cited philosopher in history? 60
    61. 61. 61
    62. 62. 62
    63. 63. even all this stuff will be compiled into the Philosophome
    64. 64. The Philosophome needs an ontology 64/
    65. 65. 65
    66. 66. philosopher instance_of 66
    67. 67. 67
    68. 68. Philonto: subtypes of philosopher 68
    69. 69. 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
    70. 70. 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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