The document discusses the importance of omics in modern biology, emphasizing the integration and tagging of biological data for enhanced discoverability and collaboration across various disciplines. It highlights the role of controlled vocabularies, such as the Gene Ontology, in linking diverse biological phenomena and datasets. The document also mentions the potential for tagging literature to improve data integration and logical reasoning in biological research.

1. The Philosophome
Barry Smith

2. Why omics?

3. Old biology data (cell division)
3

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

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. how to link the kinds of
phenomena represented here
6

7. or here
7

8. or here
8

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. or this?
10

11. or this?
11

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

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

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. coordinated tagging of
literature and data

18. coordinated tagging of literature
and data advances
•
•
•
•
discoverability
integration
logical reasoning
cross-discipinary collaboration
18

19. 19

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

25. Types of feeling in the Emotion Ontology
25

26. Types of Physiological Response to Emotion
26

27. Adam Smith
27

28. Werner
Ceusters
28

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

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

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. 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. 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. What is the Philosophome?
35/

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

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

41. 41/

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

43. 43

44. 44/

45. 45/

46. 46/

47. 47/

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/

50. 50

51. 51/

52. 52/

53. 53/

54. Continental Drift of Analytic Philosophy

55. http://philosophyideas.com/
55

56. 16,216 ideas
56/

57. pi
http://philpapers.org/
57/

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

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

61. 61

62. 62

63. even all this stuff will
be compiled into the
Philosophome

64. The Philosophome needs an
ontology
64/

65. 65

66. philosopher
instance_of
66

67. 67

68. Philonto: subtypes of philosopher
68

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. 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