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.
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
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
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
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
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/
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/
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/
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
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
Notes de l'éditeur
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
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