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Relevant Resources | ricordo.eu

Relevant Resources

TOOLS

  1. RICORDO ToolKit Home Page [https://sites.google.com/site/ricordotoolset/]
  2. RICORDO Applications [https://sites.google.com/site/ricordotoolset/applications]
  3. RICORDO Toolkit Documentation [https://sites.google.com/site/ricordotoolset/documentation]
  4. RICORDO ToolKit Code [http://code.google.com/p/ricordo/]
  5. EL-VIRA [http://code.google.com/p/el-vira/]
  6. SemGen/SemSim toolset [http://www.bhi.washington.edu/research/SemBioProcess/]
  7. SBML Harvester [http://code.google.com/p/sbmlharvester/]
  8. PhenomeBLAST [http://phenomeblast.googlecode.com]
  9. HumLoc Server for subcellular localisation prediction [http://www.cbs.dtu.dk/services/HumLoc/]

 

DELIVERABLE REPORTS

No.

 Deliverable name
D1.1

 Interim Activity report [LINK]

D1.2

  Periodic Report [LINK]
D1.3

 Interim Activity report (to be revised/accepted)
D1.4

 2nd Periodic report & associated Review Meeting (to be revised/accepted)
D1.5

 Final Report (including the Final plan for the use and dissemination foreground) (yet to be submitted)
D1.6

 Report on the distribution of the Community financial contribution between the beneficiaries (yet to be submitted)
D1.7

 3rd Periodic Report & associated Review Meeting (yet to be submitted)

D2.1

 Establish the CORDO set of dictionaries. [LINK]

D2.2

 VPH Annotation Requirements Report. [LINK]

D2.3

 VPH Technical Infrastructure Requirements Report. [LINK]
D2.4

 VPH Interoperability Plan Study Report delivered to the VPH NoE’s ToolKit Development and  Standards and Data Working Groups (yet to be submitted)

D3.1

 Technical report on VPH-wide annotation types applicable to RICORDO. [LINK]
D3.2

 Guidelines to optimise the strategy of VPHDM annotation in order to maximise interoperability  (yet to be submitted)
D3.3

 Report on effectiveness of annotation produced by RICORDO WP6-8, to inform VPH toolkit  strategy (yet to be submitted)   

D4.1

 Data exchange strategy specification. Formal document specifying the overall VPH data exchange  strategy and relevant components. [LINK]

D4.2

 Test set of RICORDO equivalence linkages and associations. [LINK]
D4.3

 Documentation of prototype RICORDO repository and web-based query system [LINK]
D4.4

 Documentation of improved RICORDO repository with computational access and query system  with interactive query construction (to be revised/accepted)
D4.5

 Update management strategy report (yet to be submitted)
D5.1

 Report on composite annotation architecture. [LINK]
D5.2

 Report on composite annotation methodologies for the VPH using CORDO Dictionary IDs (yet to  be submitted)

D6.1

 Requirements specifications for interoperability of volumetric data and models in VPH. [LINK]
D6.2

 Use Case Prototypes; covers M6.1.1, M6.2.2 and M6.3.2 (to be revised/accepted)
D6.3

 Standardisation recommendations for integration of volumetric data and models in VPH; covers  M6.1.2, M6.2.3, M6.3.3 and M6.4.1 (yet to be submitted)

D7.1

 Report on subcellular localisation prediction tools for computational pipeline. [LINK]
D7.2

 Report on the integration of subcellular prediction methods with the location annotation pipeline  and its application to the GWAS data (to be revised/accepted)
D7.3

 Report on the finalized version of the protein subcellular location pipeline (to be revised/accepted)
D7.4

 Report on the molecule-to-anatomy integration strategy (to be revised/accepted)
D8.1

 An SBML and a CellML model encoded with CORDO dictionary IDs that are also mapped to gene  expression data derived from corresponding anatomical locations (yet to be submitted)
D8.2

 Report on the systems-level model annotation strategy (yet to be submitted)

D9.1

 Report on RICORDO project website. [LINK]
D9.2

 Scientific and public dissemination report (yet to be submitted)

D9.3

  RICORDO training report, comprising at least one RICORDO training workshop (yet to be submitted)

 

MEETING DOCUMENTS

Date of meeting Documents
25th Mar 2011 1st Annual Review Presentations
23rd Apr 2012 2nd Annual Review Presentations

 

PUBLICATIONS

Adams N, Hoehndorf R, Gkoutos GV, Hansen G, Hening C.  PIDO: The Primary Immunodeficiency Disease Ontology, Bioinformatics, 2011, Sep 22, [epub ahead of print] doi: 10.1093/bioinformatics/btr531 [LINK]

Baldock RA, Burger A.  Biomedical Atlases: systematics, informatics and analysis, Advances and Experimental and Medical Biology 736 (2012) 655-677 doi: 10.1007/978-1-4419-7210-1_39  [LINK]

Bangs F, Welten M, Davey MG, Fisher M, Yin Y, Downie H, Paton B, Baldock R, Burt DW, Tickle C.  Identification of genes downstream of the Shh signalling in the developing chick wing and syn-expressed with Hoxd13 using microarray and 3D computational analysis, Mech Dev. 2010 Sep-Dec;127(9-12):428-41. Epub 2010 Aug 12., doi:10.1016/j.mod.2010.08.001

Bisbal J, Engelbrecht G, Frangi AF.  Archetype-based semantic mediation: Incremental provisioning of data services.  In the 23rd IEEE International Symposium on Computer-Based Medical Systems, 12-15, October 2010  doi: 10.1109/CBMS.2010.6042628 [LINK]

Boline JK, et al. (2010).  INCF digital atlasing program, building on Waxholm space (WHS) and the digital brain infrastructure (DAI). Society for Neuroscience 40th Annual Meeting

de Bono B, Grenon P, Sammut SJ.  ApiNATOMY: a novel toolkit for visualizing multi-scale anatomy schematics with phenotype-related information. Special Issue on Human Phenotypes, Human Mutation, Wiley  doi: 10.1002/humu.22065 [LINK]

de Bono B, Hoehndorf R, Wimalaratne S, Gkoutos G, Grenon, P (2011) The RICORDO approach to semantic interoperability for biomedical data and models: strategy, standards and solutions.  BMC Res Notes. 2011 Aug 30;4(1):313 [PMID: 21878109]

Cook DL, Bookstein FL, Gennari JH.  Physical Properties of Biological Entities: An Introduction to the Ontology of Physics for Biology, PLoS ONE, 2011. 6(12):e28708 [LINK]

Cook DL, Galdzicki M, Neal ML, Mejino JLV, Gennari JH. HeartCyc, a cardiac cycle process ontology based in the Ontology of Physics for Biology. Proceedings of the 2011 International Conference on Biomedical Ontology.  (In press)  [LINK]

Cook DL, Neal ML, Hoehndorf R, Gkoutos G, Gennari JH.  Developing a PhysioMap.  Proceedings of the 2012 ISMB BioOntologies SIG workshop.  (July 2012)

Cook, DL, Neal, ML, Hoehndorf R, Gkoutos G, Gennari JH. PhysioMaps of Physiological Processes and their Participants. Submitted to the OBML 2012 workshop (under review)

Cooling MT, Nickerson D, Miller AK, Terkildsen J, Wimalaratne S, Lloyd CM, Garny A, Crampin EJ, Nielsen P.  Best Practices for Modular Model Encoding with CellML 1.1, Hackathon on Resources for Modelling in Biology (HARMONY), New York, USA, April 2011

Cooling MT.  CellML Metadata Framework 2.0, Hackathon on Resources for Modelling in Biology (HARMONY), New York, USA, April 2011

Diez-Roux G, et al, Baldock RA, Eichele G, Ballabio A., A High-Resolution Anatomical Atlas of the Transcriptome in the Mouse Embryo, PLoS Biol 9(1) 2011: e1000582  doi:10.1371/journal.pbio.1000582 [LINK]

Fonseca CG, Backhaus M, Bluemke DA, Britten RD, Chung JD, Cowan BR, Dinov I, Finn JP, Hunter PJ, Kadish AH, Lee DC, Lima JAC, Medrano-Gracia P, Shivkumar K, Tao W, Young AA.  The Cardiac Atlas Project – An imaging database for computational modeling and statistical atlases of the heart. Bioinformatics, 2011 [PMID: 21737439]

Garny A, Cooper J, Hunter PJ.  Toward a VPH/Physiome toolkit. Wiley Interdisciplinary Reviews: Systems Biology and Medicine, 2(2): 134-147, March 2010 [LINK]

Gennari JH, Neal ML, Galdzicki M, Cook DL. (2011) Multiple Ontologies in Action: Composite Annotations for Biosimulation Models.  Journal of Biomedical Informatics, 2011 Feb;44(1):146-154. Epub 2010 Jun 30 [LINK]

Gennari JH, Neal M, Hoehndorf R, Gkoutos GV, and Cook DL.  Discovering model-model connections in biological model repositories. 2012 VPH conference (in press) 

Gianni D, McKeever S, Yu T, Britten R, Delingette H, Frangi A, Hunter P, Smith N.   Sharing and reusing cardiovascular anatomical models over the Web: a step towards the  implementation of the virtual physiological human project.  Philosophical Transactions of the Royal Society, A368(1921):3039-3056, 28 June 2010 [PMID: 20478920]

Gkoutos GV, Hoehndorf R.  Ontology-based cross-species integration and analysis of Saccharomyces cerevisiae phenotype, Proceedings of the 3rd Workshop for Ontologies in Biomedicine and Life sciences (OBML), 2011 [LINK]

Gkoutos GV, et.al. Formalisation of Saccharomyces cerevisiae phenotype representation, J. Biomedical Semantics, 2012, 3 (Suppl 2):S6

Gkoutos GV, et.al. Computational tools for comparative phenomics: the role and promise of ontologies, Mammalian Genome, 2012 [LINK]

Gkoutos GV, Schofield PN, Hoehndorf R. The Units Ontology: a tool for integrating units of measurement in science, Database, 2012, 0019.R2

Han L, van Hemert J, Baldock R. Automatically Identifying and Annotating Mouse Embryo Gene Expression Patterns, Bioinformatics 27(6) 2011, doi: 10.1093/bioinformatics/btr105 [LINK]

Hawrylycz M, Baldock RA, Burger A, Hashikawa T, Johnson GA, et al., Digital Atlasing and Standardization in the Mouse Brain., PLoS Comput Biol 7(2) 2011: e1001065, doi:10.1371/journal.pcbi.1001065 [LINK]

Ho H, Zhang C, Xie X, Hunter P.  A numerical approach to patient-specific cerebral vasospasm research.  Acta Neurochir Suppl, 110(2):157-160, 2011 [PMID: 21125463]

Hoehndorf R, Dumontier M, G. V. Gkoutos. Evaluation of biomedical ontologies, Briefings in Bioinformatics, 2012 [LINK]

Hoehndorf R, Dumontier M, G. V. Gkoutos. Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics, Bioinformatics, 2012, Aug 15;28(16):2169-75 [PMID: 22711793]

Hoehndorf R, Dumontier M, Oellrich A, Wimalaratne S, Rebholz-Schuhmann D, Schofield P, Gkoutos GV (2011)  A common layer of interoperability for biomedical ontologies based on OWL EL.  Bioinformatics  [PMID: 21343142]

Hoehndorf R, Dumontier M, Gennari JH, Wimalaratne S, de Bono B, Cook DL, Gkoutos GV.  Integrating Systems biology models and biomedical ontologies.  BMC Systems Biology, 2011. 5:124, doi:10.1186/1752-0509-5-124 [LINK]

Hoehndorf R, Dumontier M, Oellrich, Rebholz-Schuhmann AD, Schofield PN, Gkoutos GV.  Interoperability between Biomedical Ontologies through Relation Expansion, Upper-Level Ontologies and Automatic Reasoning, PLoS One. 2011;6 (7):e22006, Jul 18 [LINK]

Hoehndorf R, Oellrich, Rebholz-Schuhmann AD, Schofield PN, Gkoutos GV.  Linking PharmGKB to phenotype studies and animal models of disease for drug repurposing, Pacific Symposium of Biocomputing, 2012, 388-99 [PMID: 22174294]

Hoehndorf R, Schofield PN, Gkoutos GV.  PhenomeNET: a whole-phenome approach to disease gene discovery. Nucleic Acids Res., 2011,, Oct 1;39(18):e119 [PMID: 21737429]

Hoehndorf R, Harris MA, Herre H, Rustici G, Gkoutos GV. Semantic integration of physiology phenotypes with an application to the cellular phenotype ontology, Bioinformatics, 2012, Jul 1;28(13):1783-9 [PMID: 22539675]

Hoogendoorn C, Pashaei A, Sebastian R, Sukno FM, Camara O, and Frangi AF.  Influence of geometric variations on LV activation times: A study on an atlas-based virtual population.  In Proc. Workshop Statistical Atlases and Computational Models of the Heart (STACOM), Beijing, China, volume 6364 of Lecture Notes in Computer Science, pages 242–251, 2010 [LINK]

Hoogendoorn C, Pashaei A, Sebastian R, Sukno FM, Camara O, and Frangi AF.  Sensitivity analysis of mesh warping and subsampling strategies for generating large scale electrophysiological simulation data.  In Proc. 6th Int. Conf. on Functional Imaging and Modeling of the Heart (FIMH), New York, NY, USA, 2011. Lecture Notes in Computer Science, 2011, Volume 6666/2011, 418-426, doi: 10.1007/978-3-642-21028-0_53 [LINK]

Hunter P, Coveney PV, de Bono B, Diaz V, Fenner J, Frangi AF, Harris P, Hose R, Kohl P, Lawford P, McCormack K, Mendes M, Omholt S, Quarteroni A, Skar J, Tegner J, Randall Thomas S, Tollis I, Tsamardinos I, van Beek JH, Viceconti M.  A vision and strategy for the virtual physiological human in 2010 and beyond.  Philos Transact A Math Phys Eng Sci. 2010 Jun 13;368(1920):2595-614 [PMID: 20439264]

Juana N, Zaizi M, Burger A, Towards spatial description of biomedical atlases. In Proceedings of eHealth 2011 [LINK]

Kerwin J, Yang Y, Merchan P, Sarma S, Thompson J, Wang X, Sandoval J,  Puelles L, Baldock R, Lindsay S.  The HUDSEN Atlas: a three-dimensional (3D) spatial framework for studying gene expression in the developing human brain, J Anat. 217 no.4 (2010) 289-299, doi:10.111/j.1469-7580.2010.01290 [LINK]

McLeod K, Ferguson A, Burger A.  Argudas: arguing with gene expression information. BMC Bioinformatics 2012, 13(Suppl 1):S8 doi:10.1186/1471-2105-13-S1-S8 [LINK] 

Miller AK, Yu T, Britten R, Cooling MT, Lawson J, Cowan D, Garny A, Halstead MDB, Hunter PJ, Nickerson DP, Nunns G, Wimalaratne SM, Nielsen PMF.  Revision history aware repositories of computational models of biological systems.  BMC Bioinformatics 2011, 12:22 doi:10.1186/1471-2105-12-22 [LINK]

Nordsletten DA, Niederer SA, Nash MP, Hunter PJ, Smith N.P.   Coupling multi-physics models to cardiac mechanics.  Progress in Biophysics and Molecular Biology, 104(1-3):77-88, 2011  doi:10.1016/j.pbiomolbio.2009.11.001 [LINK]

Oellrich A, Gkoutos GV, Hoehndorf R, Rebholz-Schuhmann D.  Quantitative comparison of mapping methods between Human and Mammalian Phenotype Ontology. Proceedings of the 3rd Workshop for Ontologies in Biomedicine and Life sciences (OBML), 2011 [LINK]

Oellrich A et.al. Phenotype-based gene prioritization in mouse and man, Plos One, 2012, PLoS ONE 7(6): e38937 [LINK]

Ringwald M, Iyer V, Mason JC, Stone KR, Tadepally HD, Kadin JA, Bult CJ, Eppig JT, Oakley DJ, Briois S, Stupka E, Maselli V, Smedley D, Liu S, Hansen J, Baldock R, Hicks GG, Skarnes WC.  The IKMC web portal: a central point of entry to data and resources from the International Knockout Mouse Consortium.  Nucleic Acids Res. 2011 Jan;39(Database issue):D849-55. Epub 2010 Oct 6., doi:10.1093/nar/gkq879 [LINK]

Rubio A, de Bono AB, Nielsen H, Gupta R.  HumLoc: a one-stop shop for protein subcellular location and the effect o mutations on location.  HUPO 2011 10th Annual World COnfress, Geneva, Switzerland, 3-7 September 2011.  In Abstract Book; 2011:P131

Rubio A, de Bono AB, Nielsen H, Gupta R.  HumLoc:an integrated service for coarse-grained subcellular localisation.  Bioinformatics, ECCB 2012 (submitted)

Schofield PN, Hoehndorf R, Gkoutos GV.  Mouse genetic and phenotypic resources for human genetics, Human Mutation, 2012, Mar 15, 33(5): 826-836  doi:10.1002/humu.22077 [LINK]

Schofield P, Hoehndorf R, Gkoutos GV.  New approaches to the representation and analysis of phenotypic knowledge in human diseases and their animal models. Briefings in Functional Genomics, 2011, 10: 258-265 doi:10.1093/bfgp/elr031 [LINK]

Splendiani A, Burger A, Paschke A, Romano P, Scott Marshall M.  Biomedical semantics in the Semantic Web. Journal of Biomedical Semantics 2011, 2(Suppl 1):S1, doi:10.1186/2041-1480-2-S1-S1 [LINK]

Stevenson P, Richardson L, Venkataraman S, Yang Y, Baldock R. The BioMart interface to the eMouseAtlas gene expression database EMAGE. Database (2011) Vol. 2011 doi:10.1093/database/bar029 [LINK]

Walter T, Shattuck DW, Baldock R, Bastin ME, Carpenter AE, Duce S, Ellenberg J, Fraser A, Hamilton N, Pieper S, Ragan MA, Schneider JE, Tomancak P, Heriche J-K.  Visualization of image data from cells to organisms. Nature Methods 7 no. 3s (2010)S26-S41 doi:10.1038/nmeth.1431 [LINK]

Wang et al.  Unsupervised Segmentation and Personalised FE Modelling of In Vivo Human Myocardial Mechanics based on an MRIAtals. International Symposium on Biomedical Imaging  2012  In Press 

Wimalaratne S, Grenon P, Hoehndorf R, Gkoutos GV, de Bono B.  An infrastructure for ontology-based information systems in biomedicine: RICORDO case study, Bioinformatics (2011)28 (3):448-450  doi: 10.1093/bioinformatics/btr1591 [LINK]

Yu T, Lloyd CM, Nickerson DP, Cooling MT, Miller AK, Garny A, Terkildsen JR, Lawson J, Britten RD, Hunter PJ, Nielsen PM. The physiome model repository 2. Bioinformatics(2011) 27 (5): 743-744 doi:10.1093/bioinformatics/btq723  [LINK]

Zaslavsky I, et al. (2010).  INCF Digital Atlasing Infrastructure: Managing Interoperable Atlas Spaces.  Front Neur  doi:10.3389/conf.neuro.11.2009.08.010 [LINK]

Zaslavsky I, et al. (2010).  Representation of coordinate reference systems for the rodent brain in the INCF Digital Atlasing Infrastructure.  Front Neurosci  doi:10.3389/conf.fnins.2010.13.00135 [LINK]