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Oct 2, 2013 (3 years and 11 months ago)

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Biomax Informatics AG

Bioinformatics designed with you in mind.

FunCat
TM
, a controlled

vocabulary encompassing the
biology of prokaryotes, plants and animals from
cellular to systemic level


Dr. Dieter Maier

Manchester Ontologies Workshop 23/24.3.02

Biomax Informatics AG, Lochhamer Str. 11, 82152 Martinsried, Germany

Biomax Informatics AG

Bioinformatics designed with you in mind.

Outline


Objectives


Structure


Content


Development


Use

Biomax Informatics AG

Bioinformatics designed with you in mind.

Objectives


Automatic data management


No prior knowledge of vocabulary required


Group genes by functional categories


Extensible


Organism independent


Compatible to other ontologies

Biomax Informatics AG

Bioinformatics designed with you in mind.

Disclaimer

what the FunCat is
not
:


-
Tool for the complete description of functions on a
single gene level

Biomax Informatics AG

Bioinformatics designed with you in mind.

Structure



Organized hierarchicall



Related functions grouped on different levels



Internally consistent


=>


Provides a data warehouse


-

overview about available selection


-

progress from general to specific


-

infere from specific to general

Biomax Informatics AG

Bioinformatics designed with you in mind.

Hierarchical structure

5
´
-
end
processing

rRNA
-
processing

tRNA
-
transcription

rRNA
-
transcription

mRNA
-
transcription

mRNA
-
processing

Transcription

Biomax Informatics AG

Bioinformatics designed with you in mind.

Content


Covers cellular processes, systemic
physiology, development and anatomy


from procaryotes to the human


25 main Categories with ~ 1500


sub
-
categories


Categories are independent of organism


Genes can belong to multiple categories



Biomax Informatics AG

Bioinformatics designed with you in mind.

Metabolism: 247

Energy: 60

Cell cycle and DNA processing: 54

Transcription: 31

Protein synthesis (Translation): 11

Protein fate
(foldi
ng, modification, destination): 25

Cellular transport: 32

Cellular communication: 47

Cell rescue, defense and virulence: 50

Regulation / interaction with cellular environment: 45

Cell fate: 54

Systemic regulation / interaction with environment : 89

Development (systemic): 51

Transposable Elements, viral and plasmid proteins: 8

Control of cellular organisation: 57

Cell type differentiation: 69

Tissue differentiation: 40

Organ differentiation: 91

Enzymatic activity


=> EC ~ 4400

Protein activity regulation: 23

Protein with binding function /
cofactor requirement: 49

Transport facilitation: 49

Molecular function: 122

Biological process: 1061

Subcellular localisation: 63

Cell type localisation: 69

Tissue localisation: 41

Organ localisation: 91

Localisation: 256

Biomax Informatics AG

Bioinformatics designed with you in mind.

Development



Historical



Pathways



Thesaurus



Complex relations

Biomax Informatics AG

Bioinformatics designed with you in mind.

Structural development



Proven flexibility


easy to extend




Stable overall structure




Compatibel to other ontologies like

-

Enzyme Cataloge

-

Gene Ontology

-

EcoCyce

Biomax Informatics AG

Bioinformatics designed with you in mind.

Development in numbers


S. cerevisiae


1996



Main categories: 16


Depth:



4


Total:



182

Plant (A. thaliana)

and Procaryotes


1998




20




6




528


Animals (Human)

2001




25



6


1448


Biomax Informatics AG

Bioinformatics designed with you in mind.

Integrating Pathways into
processes

-

hierachical structure allows:

-

Univocal attribution

-

Test for completeness

-

Test for consistence

Biomax Informatics AG

Bioinformatics designed with you in mind.

Integrating additional information




Create a dynamic ontology from existing ontologies,


keywords and linguistic extraction of descriptors from


the literature




Semiautomatic mapping of dynamic ontologie to FunCat

Biomax Informatics AG

Bioinformatics designed with you in mind.

Enabling complex relations




Intensify multidimensionality




Enable
if
...
then

... relations



Biomax Informatics AG

Bioinformatics designed with you in mind.

Use



Manual annotation



Automatic annotation



Data mining

Biomax Informatics AG

Bioinformatics designed with you in mind.

Manual annotation

-

multidimensional

-

stepwise

Four
dimensions

Biomax Informatics AG

Bioinformatics designed with you in mind.

Manual annotation



17 manually annotated genomes (5 eucaryotes, 12


procaryotes)




H.sapiens, A.thaliana, S.cerevisiae, N.crassa,


propriatary: A.niger




B.subtilis, T.acidophilum, Listeria, 6 public procaryotes


in progress,


propriatary: C.glutamicum, C.pneumoniae, 1 undisclosed



Used for annotation of Transcriptomes

Biomax Informatics AG

Bioinformatics designed with you in mind.

Automatic Annotation

Sequence similarity to manually annotated proteins

(distinguish experimentally verified and similarity

associated function):


-
H. sapiens

-
A. thaliana

-
S. cerevisiae

-
B. subtilis

-
T. acidophilum

Biomax Informatics AG

Bioinformatics designed with you in mind.

PEDANT Genome Database

Currently more than 170 genomes (600 000 ORFs)

Bacteria


Archea Eucarya

Thermotogales

Flavobacteria

Cyanobacteria

Proteobacteria

Gram

positives

Green

non
-
sulfur

bacteria

Pyrodictium

Thermoproteus

Methanococcus

Methanobacterium

Methanosarcina

Extreme

halophiles

Entamoeba

Slime

molds

Animals

Fungi

Plants

Ciliates

Flagellates

Trichomonades

Microsporida

Diplomonades

Biomax Informatics AG

Bioinformatics designed with you in mind.

Data mining


Retrieval


Visualisation


Mining


Integration

Biomax Informatics AG

Bioinformatics designed with you in mind.

Queries using the FunCat:
Grouplevel

-

Looking for groups of genes:

Biomax Informatics AG

Bioinformatics designed with you in mind.

Single molecule level



-

Retrieving protein entries:

Biomax Informatics AG

Bioinformatics designed with you in mind.

The human FunCat

Unclassified

Metabolism

Energy

cell cycle

Transcription

Translation

Protein fate

Intracellular
Transport

Defense

Signalling

Cell

physiology

Biomax Informatics AG

Bioinformatics designed with you in mind.

Comparing genomes



Sequence similairty


„ functional homology“


Identification of organism specific functions

Biomax Informatics AG

Bioinformatics designed with you in mind.

Comparing H.sapiens


B.subtilis

Biomax Informatics AG

Bioinformatics designed with you in mind.

Integrative analysis

Gene expression data

Functional

catalogue

Functional

catalogue

Functional

catalogue

Functional

catalogue

Protein
-
protein

interaction data

Protein expression data

Biomax Informatics AG

Bioinformatics designed with you in mind.

Topological clustering (SOM)

Biomax Informatics AG

Bioinformatics designed with you in mind.

Distribution of the genes

Biomax Informatics AG

Bioinformatics designed with you in mind.

Limitations

Co
-
expression is no proof of functional association.




Integrate evidence from multiple sources.

Biomax Informatics AG

Bioinformatics designed with you in mind.

Integration with annotation

Analyse

gene expression data

using integration
with
annotation catalog
ue
s
.


Functional catalog
ue

Phenotypes

Interaction


Biomax Informatics AG

Bioinformatics designed with you in mind.

Functional projection

Biomax Informatics AG

Bioinformatics designed with you in mind.

Looking at the gene lists

Biomax Informatics AG

Bioinformatics designed with you in mind.

FunCat



Tool to structure information


Tool to connect information


Biomax Informatics AG

Bioinformatics designed with you in mind.

Thank

you!