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PD Map specifications

Information


Unique identifier OMICS_27732
Name PD Map
Alternative name Parkinson’s Disease Map
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Documentation


Maintainer


  • person_outline Rudi Balling

Publication for Parkinson’s Disease Map

PD Map citations

 (7)
library_books

Exploring autophagy with Gene Ontology

2018
Autophagy
PMCID: 5915032
PMID: 29455577
DOI: 10.1080/15548627.2017.1415189

[…] 000 annotations to the GOC dataset as of February 2017. UniProtKB has identifiers for all 67 human proteins in the Reactome macroautophagy pathway [] and 135 proteins associated with autophagy in the PD-map [] were downloaded. These were compared with the list of proteins annotated with the GO terms ‘autophagy’ (or one of its descendants) in the GOC database. Eight of the 67 proteins in the Reacto […]

library_books

Qualitative dynamics semantics for SBGN process description

2016
BMC Syst Biol
PMCID: 4910245
PMID: 27306057
DOI: 10.1186/s12918-016-0285-0

[…] e resulting network is a modular map of the initial comprehensive map, analogous to an influence graph. Thus, the BiNoM approach focuses on the structure of the complex and detailed network, the SBGN-PD map, by abstracting and simplifying it into an influence network in order to identify possible motifs, such as negative or positive feedback loops, that may be responsible for certain dynamics, but […]

library_books

Integration and Visualization of Translational Medicine Data for Better Understanding of Human Diseases

2016
PMCID: 4932659
PMID: 27441714
DOI: 10.1089/big.2015.0057

[…] (). The workflow is subdivided into steps from incorporation of the input files taken from tranSMART through performing the differential expression analysis and uploading the obtained results to the PD map hosted on the MINERVA platform and making them accessible for interpretation in the disease-specific context.A comparison between these two data sets provides insight about disease-related mech […]

library_books

Comparing Alzheimer’s and Parkinson’s diseases networks using graph communities structure

2016
BMC Syst Biol
PMCID: 4776441
PMID: 26935435
DOI: 10.1186/s12918-016-0270-7

[…] us sets of proteins can exert similar biological processes, such as transcription regulation, stress response and so on.Our InfoMap based computational strategy, while confirming the relevance of the PD-map by Fujita [], provided a new tool to capture the potential connection between neuronal mitochondrial dysfunction, glucose metabolism and glutamate/glutamine cycle (which also involve astroglial […]

library_books

Bioinformatics Mining and Modeling Methods for the Identification of Disease Mechanisms in Neurodegenerative Disorders

2015
Int J Mol Sci
PMCID: 4691095
PMID: 26690135
DOI: 10.3390/ijms161226148

[…] ) and all entity types (ranging from genes and proteins to cognitive testing and neuro-imaging).A “model store” harbors various disease models available to the project (AD and PD models in OpenBEL; a PD map in SBML). The model store for BEL models is based on a relational database schema, which makes this type of disease models amenable for SQL-based querying and enables an unprecedented integrati […]

library_books

Translation of SBGN maps: Process Description to Activity Flow

2013
BMC Syst Biol
PMCID: 4228393
PMID: 24176088
DOI: 10.1186/1752-0509-7-115

[…] There are many ways to translate a PD map to an AF map, depending on the level of granularity or different aspects of the map. Therefore a semi-automatic concept for the translation process was designed.The two languages have several c […]

Citations

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PD Map institution(s)
The Systems Biology Institute, Tokyo, Japan; Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg; Integrated Biobank of Luxembourg, Luxembourg City, Luxembourg; Department of Neuroscience, Centre Hospitalier Luxembourg, Luxembourg City, Luxembourg; Kodama Faculty of Medicine, Tokyo Medical and Dental University, Tokyo, Japan; Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany; Sony Computer Science Laboratories, Tokyo, Japan; Division of Systems Biology, Cancer Institute, Tokyo, Japan; Open Biology Unit, Okinawa Institute of Science and Technology, Okinawa, Japan

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