Modeling of complex systems: what is relevant?
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Modeling of complex systems: what is relevant? Arno Knobbe, Marvin Meeng, Joost Kok Leiden Institute of Advanced Computer Science (LIACS)
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Modeling of complex systems: what is relevant?. Arno Knobbe, Marvin Meeng, Joost Kok Leiden Institute of Advanced Computer Science (LIACS). Knowledge mining. Knowledge mining: Producing high-level insight by mining primary results in the context of existing knowledge. - PowerPoint PPT Presentation
Transcript of Modeling of complex systems: what is relevant?
Modeling of complex systems:what is relevant?
Arno Knobbe, Marvin Meeng, Joost KokLeiden Institute of Advanced Computer Science (LIACS)
Knowledge mining
Knowledge mining:Producing high-level insight by mining primary results in the context of existing knowledge.
Integration of detailed findings with (publicly available) domain knowledge
Knowledge sources annotations: GO, KEGG, … basic details: genomic location, … interaction networks detailed pathways: Wikipathways literature: MEDLINE
Role of LIACS in the modeling process
high-throughput datagenomics
transcriptomicsproteomics
metabolomics
important entitiesgenes
proteinsmetabolites
DataMining
DataMining
relevant conceptschromosomes
biological processespathways
transcription factorsdomain specific…
refined experimental setupselected genes
metabolitesexternal variables (O2, CO2, heat)
mathematical modelingdifferential equations
quantitative, timehigh resolution
Wikipathwaysliteraturedomain knowledge
Example: Understanding Neuroblastoma Genomic location
1. chromosome = 112. chromosome = X3. chr_arm = 11q4. chromosome = 17
GO-terms1. cell cycle2. Focal adhesion3. DNA replication4. Adherens junction
Protein families1. Cadherin_22. Cadherin3. Kinesin4. HEAT
Transcription factors1. NOVA2: Neuro-oncological
ventral antigen 2 2. Camta1: Calmodulin-
binding transcription activator 1 3. SELS Selenoprotein S
Pathways (Wikipathways)
Neoplastic processes1. Malignant Prolactinoma2. Anaplastic Oligoastrocytoma3. Adrenal neuroblastoma
Literature as Background Knowledge
concepts taken from Unified Medical Language System gene dictionary
MEDLINE abstracts Express detailed findings in terms of biological
vocabulary
Literature as Background Knowledge Biological process (4825) Molecular function (3370) Cellular component (1613)
Cell (1197) Tissue (736) Gene to gene associations (24217 other genes) Disorder (26410) Neoplastic process (4307) Pathological function (1912) …
as GO, but not annotations
Tracking concepts over time Which concepts are relevant at each timepoint? Track (multiple) winners through time Metabolic Syndrome, genes involved in fatty diet:
Contact
dr. Arno Knobbewww.liacs.nl/[email protected]
prof. dr. Joost Kokwww.liacs.nl/[email protected]
