I am an Assistant Professor at Leiden University in the Leiden Institute of Advanced Computer Science. I am a bioinformatician and my research interests are in data integration. I use scientific workflows and semantic web technologies to integrate and analyse data in systems biology and functional genomics.
SEEK ID: https://fairdomhub.org/people/132
Locations: Netherlands , Not specified
ORCID: https://orcid.org/0000-0002-1279-5133
Joined: 11th Feb 2009
Expertise: Biochemistry, Bioinformatics, Data Management
Tools: Data Management, Transcriptomics, Databases, Workflows, Web services, Taverna, Ontologies, semantic web
Related items
- Programmes (6)
- Projects (7)
- Institutions (2)
- Investigations (3)
- Studies (7)
- Assays (15)
- Data files (16+3)
- SOPs (2)
- Publications (13)
- Presentations (10+1)
NL-BioImaging AM is a distributed research infrastructure aimed at promoting progress in the most cutting edge microscopy technologies and providing open access to these technologies to a broad community of academic and industrial users. All Netherlands bio(medical) microscopy centers participate.
FAIR (Findable Accessible, Interoperable and Reusable) data management is a challenge for the optical microscopy community due to a high diversity in participating research fields and methodologies, ...
Projects: NL-Bioimaging FAIR Metadata Templates
Web page: http://eurobioimaging.nl/
Projects: Consensus Hallmark Annotation, The evolution of Gene Ontology
Web page: Not specified
FAIRDOM is establishing a support and service network for European Systems Biology. FAIRDOM is a joint action of ERA-Net ERASysAPP and European Research Infrastructure ISBE to establish a data and model management service facility for Systems Biology. Our prime mission is to support researchers, students, trainers, funders and publishers by enabling Systems Biology projects to make their Data, Operating procedures and Models, Findable, Accessible, Interoperable and Reusable (FAIR).
Projects: FAIRDOM, FAIRDOM user meeting, FAIRDOM Community Workers
Web page: http://fair-dom.org
Consortium of European research groups that aim to develop - in the forthcoming 10 years - a cluster of interlinked models that describe the whole-body human energy metabolism and its multi-dimensional regulation. Regulation includes interations with the brain, the immune system and the gut.
Projects: HUMET Startup
Web page: Not specified
Projects that do not fall under current programmes.
Projects: Manchester Institute for Biotechnology, ICYSB 2015 - International Practical Course in Systems Biology, iRhythmics, INBioPharm, EmPowerPutida, Systo models, MycoSynVac - Engineering Mycoplasma pneumoniae as a broad-spectrum animal vaccine, Multiscale modelling of state transitions in the host-microbiome-brain network, Extremophiles metabolsim, NAD COMPARTMENTATION, Agro-ecological modelling, Bergen(Ziegler lab) project AF-NADase, NAMPT affinity, Stress granules, Modelling COVID-19 epidemics, Bio-crop, ORHIZON, Coastal Data, SASKit: Senescence-Associated Systems diagnostics Kit for cancer and stroke, hybrid sequencing, HOST-PAR, BioCreative VII, Boolean modeling of Parkinson disease map, Orphan cytochrome P450 20a1 CRISPR/Cas9 mutants and neurobehavioral phenotypes in zebrafish, Selective Destruction in Ageing, Viral Metagenomic, Synthetic biology in Synechococcus for bioeconomy applications (SynEco), testproject, SDBV ephemeral data exchanges, Test project, The BeeProject, PHENET, LiceVault, EbN1 Systems Biology, UMRPégase, DeCipher, Heat stress response of the red-tide dinoflagellate Prorocentrum cordatum, middle ear, datamgmt, Institut Pasteur's projects, The nucleus of Prorocentrum cordatum, qpcr, MRC-UNICORN, Test project for Sciender, qPCR, Artificial organelles_Pathogen digestion, Supplementary Information 2 associated with the manuscript entitled " Label free Mass spectrometry proteomics reveals different pathways modulated in THP-1 cells infected with therapeutic failure and drug resistance Leishmania infantum clinical isolates", FAIR Functional Enrichment, PTPN11 mutagenesis, Supplementary Information 2 associated with the manuscript entitled "Label free Mass spectrometry proteomics reveals different pathways modulated in THP-1 cells infected with therapeutic failure and drug resistance Leishmania infantum clinical isolates", iPlacenta- Placenta on a chip, Near Surface Wave-Coherent Measurements of Temperature and Humidity, A Meta-Analysis of Functional Recovery of Aphasia after Stroke by Acupuncture Combined with Language Rehabilitation Training, Phytoplankton phenology in the Bay of Biscay: using remote sensing to assess and raise awareness of climate change impacts on the sea, Master-BIDS, Endometriosis, Vitis Data Crop, MESI-STRAT Review, Establishing an innovative and transnational feed production approach for reduced climate impact of the aquaculture sector and future food supply, ARAX: a web-based computational reasoning system for translational biomedicine, Adaptation of Salmonella enterica, I AM FRONTIER, ., PhD Nicotinic Acetylcholine Receptors, SFB1361 playground, Amaizing, Conspicuous chloroplast with LHC‒PSI/II‒megacomplex and diverse PBPs in the marine dinoflagellate Prorocentrum cordatum, icpm-kth, SDBV/HITS, sample project, TestingSeek, Genomic Medicine, Remodeling of cIV, Virtual Human Platform for Safety Assessment, PROMISEANG, URGI, Matsutake, UNDESIRABLE EFFECTS OF POST COVID-19 VACCINATION: A DESCRIPTIVE STUDY, WINTER 2022, Semantic Table Interpretation in Chemistry, MS identification of L infantum proteins related to their drug resistance patterns for new drug targets identification and ecotoxicological evaluations of their environmental and interspecies impact, the Supplementary materials for paper, ToxiGen - Reproductive toxicity and transgenerational effects of petroleum mixtures in fish, PhotoBoost, Measurement of Fisheries Provisioning Services and its Pressure to Support Sustainability of Fisheries in The Jatigede Reservoir, Indonesia, FIsh data on 2022 in the Jatigede Reservoir, ImmPort - data sharing, MESI-Review 2024, REWIRED: comparative RNA-seq and ATAC-seq in six salmonids and six outgroup telest fishes, REWIRED, Data Repository, APPN Test Project, Enhanced Anticancer Effect of Thymidylate Synthase Dimer Disrupters Promoting Intracellular Accumulation, BIDS, BioRECIPE representation format, UMass Chan BioImage DMS Core_FAIR Metadata Templates, Function, control and engineering of microbial methylotrophy, Pectobacterium pangenome, New Optical Coherence Tomography Biomarkers Identified with Deep Learning for Risk Stratification of Patients with Age-related Macular Degeneration, Virulence-related genes expression in planktonic mixed cultures of Candida albicans and non-albicans Candida species, Screening of Secondary Plant Metabolites on Antihelmintic Activity in Ascaris scum, Munich Cluster for Systems Neurology, Test project May 2024, Biospecimen Collection Protocol, Winter Wheat (Triticum aestivum L.) Grain Yield, Quality, and Net Photosynthesis When Grown Under Semi-Transparent Cadmium Telluride Photovoltaic Modules Near Maturity, Benefit for All FAIR Data, Implementation of Nanopore Sequencing for Detection of Treatment Induced Transcriptomic and Epitranscriptomic Changes in Leukaemic Tumour Models, DPL, Glycogen Metabolism in bacteria, ILS Ceramide Ring Trial, Project Test, DeepCurate, Revisiting mutational resistance to ampicillin and cefotaxime in Haemophilus influenzae, tets, Cancer Systems Biology Consortium (CSBC), Biochemical characterization of the feedforward loop between CDK1 and FOXM1 in epidermal stem cells, Drug Discovery and Biotechnology Standard Operating Procedures, EDITH (Ecosystem Digital Twins in Health) test project, Fluid flow project, Smart Garden Watering System, The role of different fatty acids, AQUACIRCLE
Web page: Not specified
SysMO is a European transnational funding and research initiative on "Systems Biology of Microorganisms".
The goal pursued by SysMO was to record and describe the dynamic molecular processes going on in unicellular microorganisms in a comprehensive way and to present these processes in the form of computerized mathematical models.
Systems biology will raise biomedical and biotechnological research to a new quality level and contribute markedly to progress in understanding. Pooling European research ...
Projects: BaCell-SysMO, COSMIC, SUMO, KOSMOBAC, SysMO-LAB, PSYSMO, SCaRAB, MOSES, TRANSLUCENT, STREAM, SulfoSys, SysMO DB, SysMO Funders, SilicoTryp, Noisy-Strep
Web page: http://sysmo.net/
FAIRDOM will establish a support and service network for European Systems Biology. We will serve projects in standardising, managing and disseminating data and models in a FAIR manner: Findable, Accessible, Interoperable and Reusable.
Organisms: Not specified
A healthy lifestyle is the basis for adequate management in cardiovascular and other chronic conditions. The BENEFIT program aims to provide long-term support to patients with cardiovascular disease (CVD) in their own home with a healthy lifestyle.The FAIR Data approach in BENEFIT standardises and structures the data collected in the project, for better use and reuse. This metadata record describes the data available and provides a contact point for researchers who would like to apply to use the ...
Programme: Independent Projects
Public web page: https://benefitforall.nl/
Organisms: Not specified
supplementary materials
Programme: Independent Projects
Public web page: Not specified
Organisms: Not specified
This project collects and maintains minimum information metadata templates designed and used in the National NL-Bioimaging initiative. The templates are based on the REMBI standards and contribute to FAIR bioimaging data in the Netherlands, together with data management in the OMERO database.
Programme: NL-Bioimaging: FAIR-DM
Public web page: http://eurobioimaging.nl/
Organisms: Not specified
Aim of HUMET Startup Project is to make an inventory of expertise, research goals, resources etc. of the HUMET Coaliytion of the Willing.
Programme: HUMET
Public web page: Not specified
Organisms: Homo sapiens
Data and experimental methods to support the work in the following paper:
Establishing Consensus Annotation for the Hallmarks of Cancer, 2020, Yi Chen, F.J.Verbeek and K.Wolstencroft, in submission
Programme: Hallmarks of cancer
Public web page: Not specified
Organisms: Homo sapiens
The main objectives of SysMO-DB are to: facilitate the web-based exchange of data between research groups within- and inter- consortia, and to provide an integrated platform for the dissemination of the results of the SysMO projects to the scientific community. We aim to devise a progressive and scalable solution to the data management needs of the SysMO initiative, that:
- facilitates and maximises the potential for data exchange between SysMO research groups;
- maximises the ‘shelf life’ and ...
Programme: SysMO
Public web page: http://www.sysmo-db.org/
Organisms: Not specified
User metadata is an essential part of experimental data. Scientists need to understand underlying conditions and experimental procedures in order to model or investigate relevant biological questions. Currently, only a small fraction of the High Content SCreening (HCS) investigations are deposited for reuse by the community, and an even smaller fraction of that data is standards-compliant. For reusing data, scientists need to be able to understand how data was generated, under which experimental ...
Submitter: Katy Wolstencroft
Studies: MIHCSME templates
Assays: General MIHCSME template, MIHCSME template example for "Integration of biological data by kernels ..., MIHCSME template example for "Uncovering the signaling landscape control..., MIHCSME template example for compound screen on HepG2 CHOP-GFP reporter ..., MIHCSME template example for “Temporal single cell cellular stress respo...
Snapshots: No snapshots
The hallmarks of cancer provide a highly cited and well-used conceptual framework for describing the processes involved in cancer cell development. However, methods for translating these high-level concepts into data-level associations between hallmarks and genes (for high throughput analysis), vary widely between studies. In this investigation we compare cancer hallmark mapping strategies from different studies, based on Gene Ontology and biological pathway annotation. By analysing the semantic ...
Submitter: Katy Wolstencroft
Studies: Comparing Cancer Hallmark Descriptions, Evolution of Gene Ontology Terms, Prognostic and Hallmark Gene Networks
Assays: Analysing Changes to GO Biological Process, Annotation Consensus and GO Consensus, Hub genes of modules and enriched GO terms, Jaccard Index Prognostic Hallmark Genes, WGCNA Prognostic Hallmark Genes
Snapshots: No snapshots
Investigating oscillations at the level of yeast populations and individual cells
Submitter: Katy Wolstencroft
Studies: Detailed kinetics of yeast glycolytic oscillation, Sustained glycolytic oscillations in individual isolated yeast cells
Assays: Detailed kinetic model of yeast glycolytic oscillation, Metabolite concentrations in yeast glycolytic oscillations, Modelling sustained glycolytic oscillations in individual isolated yeast...
Snapshots: No snapshots
The hallmarks mapping schemes under comparison were developed over the period of 7 years and therefore were developed using different versions of the Gene Ontology and associated annotation. Understanding which differences between mapping schemes were the result of topological or annotation changes to GO could therefore help to further refine consensus and make results and conclusions more comparable between studies.
Submitter: Katy Wolstencroft
Investigation: Cancer Hallmark Consensus
Snapshots: No snapshots
Multiple studies have devised mapping schemes to associate cancer hallmarks with Gene Ontology terms and biological pathway. This study compares the similarities and differences between them, in order to establish consensus knowledge.
Submitter: Katy Wolstencroft
Investigation: Cancer Hallmark Consensus
Snapshots: No snapshots
This study examines how different hallmark gene datasets intersect with prognostic cancer genes
Submitter: Katy Wolstencroft
Investigation: Cancer Hallmark Consensus
Assays: Hub genes of modules and enriched GO terms, Jaccard Index Prognostic Hallmark Genes, WGCNA Prognostic Hallmark Genes
Snapshots: No snapshots
Here you will find guidelines for creating MIAPE compliant proteomics data files as well as examples and links to online tools and resources
Submitter: Katy Wolstencroft
Investigation: Creating data sheet template for 'omics data
Assays: Proteomics Template (gel electrophoresis), Proteomics Templates (Mass spectrometry)
Snapshots: No snapshots
Here you will find guidelines for creating MAGE-TAB compliant transcriptomics data files as well as examples and links to online tools and resources.
Submitter: Katy Wolstencroft
Investigation: Creating data sheet template for 'omics data
Assays: Affy Transcriptomics Templates, Chip-chip Excel Template, General Transcriptomics Templates, NimbleGen Transcriptomics Templates, RT-PCR Excel Template
Snapshots: No snapshots
Submitter: Katy Wolstencroft
Investigation: Yeast Glycolytic Oscillations
Assays: Detailed kinetic model of yeast glycolytic oscillation, Metabolite concentrations in yeast glycolytic oscillations
Snapshots: No snapshots
Submitter: Katy Wolstencroft
Investigation: Yeast Glycolytic Oscillations
Assays: Modelling sustained glycolytic oscillations in individual isolated yeast...
Snapshots: No snapshots
Some generic examples of transcriptomics templates that conform to the MAGE-TAB specification. These templates were created and modified from templates produced by ArrayExpress and GEO. These templates are generic and non-specific for any particular array platform.
Submitter: Katy Wolstencroft
Assay type: Transcriptomics
Technology type: Microarray
Investigation: Creating data sheet template for 'omics data
Organisms: No organisms
SOPs: Transcriptomics Template Guidelines
Data files: Transcriptomics Template (ArrayExpress Format)
Snapshots: No snapshots
Some examples of proteomics templates for Mass Spectrometry data that conform to the MIAPE specification
Submitter: Katy Wolstencroft
Assay type: Proteomics
Technology type: Mass Spectrometry
Investigation: Creating data sheet template for 'omics data
Organisms: No organisms
SOPs: Guidelines for Proteomics Templates
Data files: Proteomics Mass Spec Template (SysMO JERM), Proteomics Template (empty) from PRIDE, Proteomics Template from PRIDE
Snapshots: No snapshots
This Excel template is the general (master) template for any type of metabolomics data. It can be used as it is, or extended and modified to create a more specific templates for particular technologies and assay types.
Submitter: Katy Wolstencroft
Assay type: Metabolomics
Technology type: Technology Type
Investigation: Creating data sheet template for 'omics data
Organisms: No organisms
SOPs: No SOPs
Data files: Metabolomics Master Excel Template and 1 hidden item
Snapshots: No snapshots
Some examples of transcriptomics templates for Affymetrix data that conform to the MAGE-TAB specification. These templates were taken from the GEO website (http://www.ncbi.nlm.nih.gov/geo/info/spreadsheet.html) and modified to conform to the SysMO-JERM (Just enough Results Model) for transcriptomics. Using these templates will mean easier submission to GEO/ArrayExpress and greater consistency of data in SEEK.
Submitter: Katy Wolstencroft
Assay type: Transcriptomics
Technology type: Microarray
Investigation: Creating data sheet template for 'omics data
Organisms: No organisms
SOPs: Transcriptomics Template Guidelines
Data files: 3' or Whole Gene Expression Array Template (Aff..., Chip-chip Array Template (Affymetrix)
Snapshots: No snapshots
A example of an RT-PCR Excel template. RT-PCR is Reverse Transcriptase PCR (NOT to be confused with Real Time PCR, which is normally referred to as qPCR)
This template was taken from the GEO website (http://www.ncbi.nlm.nih.gov/geo/info/spreadsheet.html) and modified to conform to the SysMO-JERM (Just enough Results Model) for transcriptomics. Using templates will mean easier submission to public databases on publication and greater consistency of data in SEEK.
Submitter: Katy Wolstencroft
Assay type: Gene Expression Profiling
Technology type: qRT-PCR
Investigation: Creating data sheet template for 'omics data
Organisms: No organisms
SOPs: Transcriptomics Template Guidelines
Data files: RT-PCR Excel Template
Snapshots: No snapshots
This Excel template is an example taken from the GEO web site (http://www.ncbi.nlm.nih.gov/geo/info/spreadsheet.html#GAtemplates) which has been modified to conform to the SysMO JERM (Just Enough Results Model). Using templates helps with searching and comparing data as well as making it easier to submit data to public repositories for publications.
Submitter: Katy Wolstencroft
Assay type: Transcriptomics
Technology type: ChIP-on-chip
Investigation: Creating data sheet template for 'omics data
Organisms: No organisms
SOPs: Transcriptomics Template Guidelines
Data files: Chip-chip Excel template example
Snapshots: No snapshots
Some examples of transcriptomics templates for NimbleGen data that conform to the MAGE-TAB specification. These templates were taken from the GEO website (http://www.ncbi.nlm.nih.gov/geo/info/spreadsheet.html) and modified to conform to the SysMO-JERM (Just enough Results Model) for transcriptomics. Using templates will mean easier submission to GEO/ArrayExpress upon publication and greater consistency of data in SEEK for easier searching and comparing.
Submitter: Katy Wolstencroft
Assay type: Transcriptomics
Technology type: Microarray
Investigation: Creating data sheet template for 'omics data
Organisms: No organisms
SOPs: No SOPs
Data files: Genomic Data Submission Excel Template (NimbleGen), Transcriptomics Gene Expression Excel Template ...
Snapshots: No snapshots
Examples of proteomics templates for gele electrophoresis data that conform to the MIAPE-GE specification
Submitter: Katy Wolstencroft
Assay type: Proteomics
Technology type: Electrophoresis
Investigation: Creating data sheet template for 'omics data
Organisms: No organisms
SOPs: No SOPs
Data files: Proteomics Gel Electrophoresis Excel Template, Template for proteomics (2D gel)
Snapshots: No snapshots
Submitter: Katy Wolstencroft
Biological problem addressed: Model Analysis Type
Investigation: Yeast Glycolytic Oscillations
Organisms: No organisms
Models: Sustained glycolytic oscillations in individual..., Sustained glycolytic oscillations in individual..., Sustained glycolytic oscillations in individual..., Sustained glycolytic oscillations in individual...
SOPs: No SOPs
Data files: No Data files
Snapshots: No snapshots
Submitter: Katy Wolstencroft
Biological problem addressed: Model Analysis Type
Investigation: Yeast Glycolytic Oscillations
Organisms: Saccharomyces cerevisiae
Models: Detailed kinetic model of yeast glycolytic osci..., Detailed kinetic model of yeast glycolytic osci..., Detailed kinetic model of yeast glycolytic osci..., Detailed kinetic model of yeast glycolytic osci..., Detailed kinetic model of yeast glycolytic osci..., Detailed kinetic model of yeast glycolytic osci..., Detailed kinetic model of yeast glycolytic osci...
SOPs: No SOPs
Data files: Das (1991) NADH and ATP concentrations determin..., Das (1991) Time varying concentrations for meta..., Richard (1996) Concentrations of oscillating gl... and 7 hidden items
Snapshots: No snapshots
Concentration of glycolytic intermediates over time
Submitter: Katy Wolstencroft
Assay type: Discontinuous Enzymatic
Technology type: Enzymatic Activity Measurements
Investigation: Yeast Glycolytic Oscillations
Organisms: Saccharomyces cerevisiae
SOPs: No SOPs
Data files: Das (1991) NADH and ATP concentrations determin..., Richard (1996) Concentrations of oscillating gl...
Snapshots: No snapshots
Submitter: Katy Wolstencroft
Biological problem addressed: Annotation
Investigation: Cancer Hallmark Consensus
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: GO Consensus terms, Genes annotated to selected GO terms belonging ..., Hallmark genes, Mapping from Gene Ontology terms to individual ..., Mapping from MSigDB pathways to GO terms, Mapping from pathways to individual cancer hall..., The number of genes annotated to individual can...
Snapshots: No snapshots
A Weighted Gene Co-Expression Network Analysis (WGCNA) of breast cancer prognostic genes (derived from transcriptome data from the TCGA Genomics Data Commons (GDC) data portal (https://portal.gdc.cancer.gov/)), and cancer hallmark genes.
Submitter: Katy Wolstencroft
Biological problem addressed: Biological Network Analysis
Investigation: Cancer Hallmark Consensus
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: FPKM value of breast cancer patient, Prognostic-hallmark genes of GO1 with log trans..., Prognostic-hallmark genes of GO2 with log trans..., Prognostic-hallmark genes of GO3 with log trans..., Prognostic-hallmark genes of GO4 with log trans...
Snapshots: No snapshots
A Jaccard Index of the overlap between prognostic and hallmark genes for 17 cancer types across different mapping schemes. The impact of selecting different mapping schemes was assessed by pairwise comparisons where there were 5 or more shared genes.
Submitter: Katy Wolstencroft
Biological problem addressed: Biological Network Analysis
Investigation: Cancer Hallmark Consensus
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: Abbreviations of 17 cancer types, Jaccard index score, prognostic genes of 17 cancer types
Snapshots: No snapshots
Submitter: Katy Wolstencroft
Biological problem addressed: Biological Network Analysis
Investigation: Cancer Hallmark Consensus
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: Edge data of GO terms in 2012, Edge data of GO terms in 2016, GO hierarchical network comparison between methods, Gene product count of GO terms in June 2012., Species data in June,2012, Term description and ID in June 2016, Term description and ID in June,2012, The number of annotations belongs to selected G..., species data in June, 2016, species data of GO in 2016, species data of GO in 2016
Snapshots: No snapshots
An example template for MAGE-TAB compliant transcriptomics data. This example only covers the Investigation Description Format (IDF) and the Sample and Data Relationship Format (SDRF) worksheets (i.e. the metadata from a microarray experiment). This template was generated automatically using the ArrayExpress submission help tool (http://www.ebi.ac.uk/cgi-bin/microarray/magetab.cgi)
Creators: Katy Wolstencroft, Olga Krebs
Submitter: Katy Wolstencroft
An example of a JERM-compliant template for RT-PCR data
This template was taken from the GEO website (http://www.ncbi.nlm.nih.gov/geo/info/spreadsheet.html) and modified to conform to the SysMO-JERM (Just enough Results Model) for transcriptomics.
Creator: Katy Wolstencroft
Submitter: Katy Wolstencroft
Investigations: Creating data sheet template for 'omics data
Studies: Creating Templates for Transcriptomics
Assays: RT-PCR Excel Template
An example of a blank data sheet for Mass spectrometry data. This is not SysMO specific, but it is an example of MIAPE compliant data.
The shreadsheet contains macros to help you annotate your data with terms from controlled vocabularies and ontologies
Creator: Katy Wolstencroft
Submitter: Katy Wolstencroft
Investigations: Creating data sheet template for 'omics data
Studies: Creating Templates for Proteomics
Excel sheet template : concentrations of intracellular metabolites
Creators: Olga Krebs, Katy Wolstencroft
Submitter: Olga Krebs
Investigations: Creating data sheet template for 'omics data and 1 hidden item
Studies: Creating template for metabolomics data and 1 hidden item
Assays: Standard-based Excel template for metabolomics ... and 2 hidden items
This Excel template is the general (master) template for any type of metabolomics data. It can be used as it is, or extended and modified to create a more specific templates for particular technologies and assay types.
Creators: Katy Wolstencroft, Olga Krebs
Submitter: Katy Wolstencroft
Investigations: Creating data sheet template for 'omics data
Studies: Creating template for metabolomics data
Assays: Metabolomics Master Template
Report of the Data Management Foundry Workshop, 19th-20th of March, 2012, Vienna, Austria
Creators: Natalie Stanford, Katy Wolstencroft, Olga Krebs, Stuart Owen, Carole Goble, Wolfgang Müller
Submitter: Natalie Stanford
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
This is an Excel template for Mass Spec data that contains all the necessary MIAPE metadata fields. It was derived from examples on the PRIDE website (PRoteomics IDEntifications database http://www.ebi.ac.uk/pride/)
Creator: Katy Wolstencroft
Submitter: Katy Wolstencroft
Investigations: Creating data sheet template for 'omics data
Studies: Creating Templates for Proteomics
An example of a completed data sheet for Mass spectrometry data. This is not SysMO specific, but it is an example of a MIAPE compliant data format taken from the PRIDE website (http://www.ebi.ac.uk/pride).
Creator: Katy Wolstencroft
Submitter: Katy Wolstencroft
Investigations: Creating data sheet template for 'omics data
Studies: Creating Templates for Proteomics
This template is a JERM compliant spreadsheet for use with gel electrophoresis data. It is in the style of the JERM MASTER template with worksheets for metadata, organism_sample, instrument and data. To conform to MIAPE-GE all worksheets are mandatory. A detailed description of MIAPE-GE is available from http://www.psidev.info/miape/MIAPE_GE_1_4.pdf
Creator: Katy Wolstencroft
Submitter: Katy Wolstencroft
Investigations: Creating data sheet template for 'omics data
Studies: Creating Templates for Proteomics
This report gives an overview of the sessions and outcomes from the recent SEEK Users meeting in Berlin. Please see related 'Presentation' entries for related slides and supplementary material.
Creator: Katy Wolstencroft
Submitter: Katy Wolstencroft
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
This Excel template is for use with affy transcriptomics data in Matrix table format. It was created from a template on the GEO web site (http://www.ncbi.nlm.nih.gov/geo/info/geo_affy.html) and modified to conform to the SysMO JERM for transcriptomics.
Creator: Katy Wolstencroft
Submitter: Katy Wolstencroft
Investigations: Creating data sheet template for 'omics data
Studies: Creating Templates for Transcriptomics
Assays: Affy Transcriptomics Templates
This Excel template is for use with affy Chip-chip data where the results of the primary analysis are reported in BAR and BED files. It was created from a template on the GEO web site (http://www.ncbi.nlm.nih.gov/geo/info/geo_affy.html) and modified to conform to the SysMO JERM for transcriptomics.
Creator: Katy Wolstencroft
Submitter: Katy Wolstencroft
Investigations: Creating data sheet template for 'omics data
Studies: Creating Templates for Transcriptomics
Assays: Affy Transcriptomics Templates
This Excel template is an example taken from the GEO web site (http://www.ncbi.nlm.nih.gov/geo/info/spreadsheet.html#GAtemplates) which has been modified to conform to the SysMO JERM (Just Enough Results Model). Using templates helps with searching and comparing data as well as making it easier to submit data to public repositories for publications.
Creator: Katy Wolstencroft
Submitter: Katy Wolstencroft
Investigations: Creating data sheet template for 'omics data
Studies: Creating Templates for Transcriptomics
Assays: Chip-chip Excel Template
This template is for recording gene expression data from the NimbleGen platform. This template was taken from the GEO website (http://www.ncbi.nlm.nih.gov/geo/info/spreadsheet.html) and modified to conform to the SysMO-JERM (Just enough Results Model) for transcriptomics. Using these templates will mean easier submission to GEO/ArrayExpress and greater consistency of data in SEEK.
Creator: Katy Wolstencroft
Submitter: Katy Wolstencroft
Investigations: Creating data sheet template for 'omics data
This template is for recording genome data from the NimbleGen platform. This template was taken from the GEO website (http://www.ncbi.nlm.nih.gov/geo/info/spreadsheet.html) and modified to conform to the SysMO-JERM (Just enough Results Model) for transcriptomics. Using these templates will mean easier submission to GEO/ArrayExpress and greater consistency of data in SEEK.
Creator: Katy Wolstencroft
Submitter: Katy Wolstencroft
Investigations: Creating data sheet template for 'omics data
This document outlines our plans for making it easier to publish assets from SEEK to enable people from outside the consortium to see them.
Creator: Katy Wolstencroft
Submitter: Katy Wolstencroft
Investigations: No Investigations
Studies: No Studies
Assays: No Assays
An overview of creating MAGE-TAB compliant spreadsheets for transcriptomics data in SysMO SEEK
Creator: Katy Wolstencroft
Submitter: Katy Wolstencroft
MIAPE (Minimum Information About a Proteomics Experiment) is the recommended format for proteomics data in SysMO-SEEK. The document attached provides more information and links to tools and resources.
Creator: Katy Wolstencroft
Submitter: Katy Wolstencroft
Investigations: Creating data sheet template for 'omics data
Studies: Creating Templates for Proteomics
Abstract (Expand)
Authors: K. Wolstencroft, O. Krebs, J. L. Snoep, N. J. Stanford, F. Bacall, M. Golebiewski, R. Kuzyakiv, Q. Nguyen, S. Owen, S. Soiland-Reyes, J. Straszewski, D. D. van Niekerk, A. R. Williams, L. Malmstrom, B. Rinn, W. Muller, C. Goble
Date Published: 4th Jan 2017
Publication Type: Journal
PubMed ID: 27899646
Citation: Nucleic Acids Res. 2017 Jan 4;45(D1):D404-D407. doi: 10.1093/nar/gkw1032. Epub 2016 Nov 28.
Abstract (Expand)
Authors: K. Wolstencroft, O. Krebs, J. L. Snoep, N. J. Stanford, F. Bacall, M. Golebiewski, R. Kuzyakiv, Q. Nguyen, S. Owen, S. Soiland-Reyes, J. Straszewski, D. D. van Niekerk, A. R. Williams, L. Malmstrom, B. Rinn, W. Muller, C. Goble
Date Published: 4th Jan 2017
Publication Type: Journal
PubMed ID: 27899646
Citation: Nucleic Acids Res. 2017 Jan 4;45(D1):D404-D407. doi: 10.1093/nar/gkw1032. Epub 2016 Nov 28.
Abstract (Expand)
Authors: M. D. Wilkinson, M. Dumontier, I. J. Aalbersberg, G. Appleton, M. Axton, A. Baak, N. Blomberg, J. W. Boiten, L. B. da Silva Santos, P. E. Bourne, J. Bouwman, A. J. Brookes, T. Clark, M. Crosas, I. Dillo, O. Dumon, S. Edmunds, C. T. Evelo, R. Finkers, A. Gonzalez-Beltran, A. J. Gray, P. Groth, C. Goble, J. S. Grethe, J. Heringa, P. A. 't Hoen, R. Hooft, T. Kuhn, R. Kok, J. Kok, S. J. Lusher, M. E. Martone, A. Mons, A. L. Packer, B. Persson, P. Rocca-Serra, M. Roos, R. van Schaik, S. A. Sansone, E. Schultes, T. Sengstag, T. Slater, G. Strawn, M. A. Swertz, M. Thompson, J. van der Lei, E. van Mulligen, J. Velterop, A. Waagmeester, P. Wittenburg, K. Wolstencroft, J. Zhao, B. Mons
Date Published: 15th Mar 2016
Publication Type: Journal
PubMed ID: 26978244
Citation: Sci Data. 2016 Mar 15;3:160018. doi: 10.1038/sdata.2016.18.
Abstract (Expand)
Authors: , , Matthew Horridge, Simon Jupp, , , , , Robert Stevens,
Date Published: 1st Feb 2013
Publication Type: Journal
DOI: 10.1002/cpe.2941
Citation: Concurrency Computat.: Pract. Exper. 25(4):467-480
Abstract (Expand)
Authors: Susanna-Assunta Sansone, Philippe Rocca-Serra, Dawn Field, Eamonn Maguire, Chris Taylor, Oliver Hofmann, Hong Fang, Steffen Neumann, Weida Tong, Linda Amaral-Zettler, Kimberly Begley, Tim Booth, Lydie Bougueleret, Gully Burns, Brad Chapman, Tim Clark, Lee-Ann Coleman, Jay Copeland, Sudeshna Das, Antoine de Daruvar, Paula de Matos, Ian Dix, Scott Edmunds, Chris T Evelo, Mark J Forster, Pascale Gaudet, Jack Gilbert, , Julian L Griffin, Daniel Jacob, Jos Kleinjans, Lee Harland, Kenneth Haug, Henning Hermjakob, Shannan J Ho Sui, Alain Laederach, Shaoguang Liang, Stephen Marshall, Annette McGrath, Emily Merrill, Dorothy Reilly, Magali Roux, Caroline E Shamu, Catherine A Shang, Christoph Steinbeck, Anne Trefethen, Bryn Williams-Jones, , Ioannis Xenarios, Winston Hide
Date Published: 28th Jan 2012
Publication Type: Not specified
PubMed ID: 22281772
Citation:
Abstract (Expand)
Authors: Simon Jupp, Matthew Horridge, Luigi Iannone, Julie Klein, , Joost Schanstra, , Robert Stevens
Date Published: 25th Jan 2012
Publication Type: Not specified
PubMed ID: 22373396
Citation:
Abstract (Expand)
Authors: Katy Wolstencroft, Stuart Owen, Matthew Horridge, Wolfgang Mueller, Finn Bacall, Jacky Snoep, Franco du Preez, Quyen Nguyen, Olga Krebs, Carole Goble
Date Published: 2012
Publication Type: Journal
DOI: 10.1007/978-3-642-33876-2_42
Citation: Knowledge Engineering and Knowledge Management 7603:438-441,Springer Berlin Heidelberg
Abstract (Expand)
Authors: Dagmar Waltemath, Richard Adams, Frank T Bergmann, Michael Hucka, Fedor Kolpakov, Andrew K Miller, Ion I Moraru, David Nickerson, Sven Sahle, , Nicolas Le Novère
Date Published: 15th Dec 2011
Publication Type: Not specified
PubMed ID: 22172142
Citation:
Abstract (Expand)
Editor:
Date Published: 28th Sep 2011
Publication Type: Journal
PubMed ID: 21943917
Citation: Methods Enzymol. 2011;500:629-55. doi: 10.1016/B978-0-12-385118-5.00029-3.
Abstract (Expand)
Authors: Suzanne Geenen, , Michael Reed, H Frederik Nijhout, J Gerry Kenna, Ian D Wilson, ,
Date Published: 24th Aug 2011
Publication Type: Not specified
PubMed ID: 21888969
Citation:
Abstract (Expand)
Authors: , , Matthew Horridge, , , , ,
Date Published: 15th Jul 2011
Publication Type: Journal
PubMed ID: 21622664
Citation: Bioinformatics. 2011 Jul 15;27(14):2021-2. doi: 10.1093/bioinformatics/btr312. Epub 2011 May 26.
Abstract (Expand)
Authors: Alexey Kolodkin, Fred C Boogerd, Nick Plant, Frank J Bruggeman, Valeri Goncharuk, Jeantine Lunshof, Rafael Moreno-Sanchez, Nilgun Yilmaz, Barbara M Bakker, , Rudi Balling,
Date Published: 16th Jun 2011
Publication Type: Not specified
PubMed ID: 21704158
Citation:
Abstract (Expand)
Editor:
Date Published: 4th Dec 2009
Publication Type: Not specified
PubMed ID: 19954172
Citation:
FAIRDOM introduction by Olga Krebs
Creators: Olga Krebs, Carole Goble, Katy Wolstencroft
Submitter: Olga Krebs
Presentation by Carole Goble at the International Semantic Web Conference 2013 in Sydney Australia about the use of semantic web technology in SEEK and RightField.
Creators: Stuart Owen, Carole Goble, Katy Wolstencroft, Jacky Snoep, Wolfgang Müller, Olga Krebs, Quyen Nguyen
Submitter: Stuart Owen
Introduction to RightField and Demo were presented at the Virtual Liver Network PALs meeting on 31st of October in Hünfeld, Germany
Creators: Olga Krebs, Stuart Owen, Katy Wolstencroft
Submitter: Olga Krebs
Katy Wolstencroft's talk at the "3rd Eagle Genomics Symposium:Will Big Data and Bigger Cuts Cripple Bioinformatics?", presented on 21st March 2013.
Creator: Katy Wolstencroft
Submitter: Stuart Owen
This document is a summary of the SysMO-DB PALs meeting on the 29-30 November 2012
Creators: Katy Wolstencroft, Olga Krebs, Stuart Owen
Submitter: Katy Wolstencroft
Issues and considerations for data management as SysMO projects approach the end of their funding
Creator: Katy Wolstencroft
Submitter: Katy Wolstencroft
This talk was presented at the IEEE e-Science conference, Chicago, USA (8-12 October 2012). http://www.ci.uchicago.edu/escience2012/ It describes the latest developments in RightField for both semantic data annotation and extraction to RDF.
Creators: Katy Wolstencroft, Stuart Owen, Carole Goble
Submitter: Katy Wolstencroft
SEEK at ICSB 2012 (presented by Olga Krebs)
Creators: Olga Krebs, Katy Wolstencroft, Carole Goble, Wolfgang Müller, Quyen Nguyen, Stuart Owen, Jacky Snoep, Franco du Preez, Martin Golebiewski, Andreas Weidemann
Submitter: Olga Krebs
An overview of the SEEK for the HCLS Systems Biology Task force meeting
Creators: Katy Wolstencroft, Stuart Owen
Submitter: Katy Wolstencroft
This presentation gives an overview of the way we structure and share data in the SEEK using JERM templates, and how we use the ISA hierarchy of Investigations, Studies, and Assays to associate experiments and data sets together. These slides were presented at the SEEK Users meeting in Berlin 2012.
Creator: Katy Wolstencroft
Submitter: Katy Wolstencroft