Tag: Knowledge

pathClass 0.9.4 – Classification using Biological Pathways as prior knowledge

pathClass 0.9.4

:: DESCRIPTION

pathClass is a collection of classification methods that use information about feature connectivity in a biological network as an additional source of information. This additional knowledge is incorporated into the classification a priori. Several authors have shown that this approach significantly increases the classification performance.

::DEVELOPER

pathClass team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R

:: DOWNLOAD

 pathClass

:: MORE INFORMATION

Citation

Bioinformatics. 2011 May 15;27(10):1442-3. doi: 10.1093/bioinformatics/btr157. Epub 2011 Mar 30.
pathClass: an R-package for integration of pathway knowledge into support vector machines for biomarker discovery.
Johannes M1, Fröhlich H, Sültmann H, Beissbarth T.

KDDN 1.1.0 – Knowledge-fused Differential Dependency Network

KDDN 1.1.0

:: DESCRIPTION

KDDN is a Cytoscape app to learn biological network topology and its changes using profiling data and domain knowledge. It takes input data and runs KDDN algorithm to construct the dependency network.

::DEVELOPER

KDDN team

:: SCREENSHOTS

KDDN

:: REQUIREMENTS

  • Windows / Linux/ MacOsX
  • Java
  • Cytoscape

:: DOWNLOAD

 KDDN

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Sep 30. pii: btu632. [Epub ahead of print]
KDDN: an open-source Cytoscape app for constructing differential dependency networks with significant rewiring.
Tian Y, Zhang B, Hoffman EP, Clarke R, Zhang Z, Shih IM, Xuan J, Herrington DM, Wang Y.

GPKB – Genomic and Proteomic Knowledge Base

GPKB

:: DESCRIPTION

GPKB integrates several of the most relevant sources of such dispersed information (including Entrez Gene, UniProt, IntAct, Expasy Enzyme, GO, GOA, BioCyc, KEGG, Reactome, and OMIM).

::DEVELOPER

GPKB team

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Masseroli M, Canakoglu A, Ceri S.
Integration and Querying of Genomic and Proteomic Semantic Annotations for Biomedical Knowledge Extraction.
IEEE/ACM Trans Comput Biol Bioinform. 2016 Mar-Apr;13(2):209-19. doi: 10.1109/TCBB.2015.2453944. PMID: 27045824.

KMAD 1.15 – Knowledge Based Multiple Sequence Alignment for Intrinsically Disordered Proteins

KMAD 1.15

:: DESCRIPTION

KMAD was designed to align intrinsically disordered (aka natively unfolded) proteins for the HOPE mutation analysis server.

::DEVELOPER

KAMD Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 KMAD

:: MORE INFORMATION

Citation

KMAD: Knowledge based multiple sequence alignment for intrinsically disordered proteins.
Lange J, Wyrwicz LS, Vriend G.
Bioinformatics. 2015 Nov 14. pii: btv663.

TADKB – Topologically Associating Domain Knowledge Base

TADKB

:: DESCRIPTION

TADKB is an integrated resource for exploring topologically associating domains (TADs)

::DEVELOPER

Z. WANG LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Liu T, Porter J, Zhao C, Zhu H, Wang N, Sun Z, Mo YY, Wang Z.
TADKB: Family classification and a knowledge base of topologically associating domains.
BMC Genomics. 2019 Mar 14;20(1):217. doi: 10.1186/s12864-019-5551-2. PMID: 30871473; PMCID: PMC6419456.

Harmonizome 1.5 – Integrated Knowledge About Genes & Proteins

Harmonizome 1.5

:: DESCRIPTION

Harmonizome is a collection of processed datasets gathered to serve and mine knowledge about genes and proteins from over 70 major online resources.

::DEVELOPER

Ma’ayan Laboratory

:: SCREENSHOTS

:: REQUIREMENTS

  • Web Server

:: DOWNLOAD

Harmonizome 

:: MORE INFORMATION

Citation

Database (Oxford). 2016 Jul 3;2016. pii: baw100. doi: 10.1093/database/baw100. Print 2016.
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins.
Rouillard AD, Gundersen GW, Fernandez NF, Wang Z, Monteiro CD, McDermott MG, Ma’ayan A.

BioMyn – Mining Gene and Protein Knowledge

BioMyn

:: DESCRIPTION

BioMyn is a comprehensive online resource that integrates information related to human genes and proteins from over a dozen external databases. It includes Gene Ontology annotations of human genes and proteins, sequence family classifications, protein domain architectures, metabolic and signaling pathways, protein interactions and protein complexes, and disease associations.

::DEVELOPER

Max-Planck-Institut Informatik

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 BioMyn

:: MORE INFORMATION