supplementary materials
Programme: Independent Projects
SEEK ID: https://fairdomhub.org/projects/320
Public web page: Not specified
Organisms: No Organisms specified
FAIRDOM PALs: No PALs for this Project
Project created: 28th Nov 2022
Related items
- People (2)
- Programmes (1)
- Institutions (1)
- Investigations (1)
- Studies (1)
- Assays (1)
- Data files (2)
- Documents (2)
Projects: Consensus Hallmark Annotation, FAIR Functional Enrichment
Institutions: University of Leiden, LIACS
Projects: SysMO DB, HUMET Startup, FAIRDOM, Consensus Hallmark Annotation, NL-Bioimaging FAIR Metadata Templates, FAIR Functional Enrichment
Institutions: University of Leiden, LIACS

Expertise: Biochemistry, Bioinformatics, Data Management
Tools: Data Management, Transcriptomics, Databases, Workflows, Web services, Taverna, Ontologies, semantic web
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.
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, UMRPƩgase, 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
Web page: Not specified
This investigation serves as supplementary material for a SWAT4HCLS publication that describes minimum metadata and provenance requirements for reproducible enrichment analysis results.
Functional enrichment analysis is an essential downstream process in high throughput omics studies, such as transcriptomics and proteomics. By using the Gene Ontology (GO) and its annotations (GOA), underlying functional patterns of over-representation can be identified, leading to ...
Snapshots: No snapshots
This study describes the results of a survey on enrichment analysis tool usage and provenance reporting for a corpus of SARS-CoV2 data.
Submitter: Yi Chen
Investigation: FAIR Functional Enrichment: Assessing and Model...
Assays: FAIR Functional Enrichment
Snapshots: No snapshots
Submitter: Yi Chen
Biological problem addressed: Gene Expression
Investigation: FAIR Functional Enrichment: Assessing and Model...
Study: FAIR Functional Enrichment
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: Supplementary file 1: Search Terms, Supplementary file 2: Publications surveyed
Snapshots: No snapshots
This file provides a full list of the PubMed IDs used as input to our survey of SARS-CoV2 enrichment analysis results
Creators: None
Submitter: Yi Chen
Investigations: FAIR Functional Enrichment: Assessing and Model...
Studies: FAIR Functional Enrichment
Assays: FAIR Functional Enrichment
A list of the search terms used for identifying SARS-CoV2 studies involving enrichment analysis. A random sample of 100 papers were used as input to the experiment.
Creators: None
Submitter: Yi Chen
Investigations: FAIR Functional Enrichment: Assessing and Model...
Studies: FAIR Functional Enrichment
Assays: FAIR Functional Enrichment
Figures showing the changes of edges and terms.
Investigations: FAIR Functional Enrichment: Assessing and Model...
Studies: FAIR Functional Enrichment
Assays: FAIR Functional Enrichment
Prov-O Representation for an enrichment analysis experiment on differentially expressed RNA-Seq data, analysed with Enrichr and 2021 version of GO. Rectangle represents Activity, eclipse represents entity and rhombus represents agents
Investigations: FAIR Functional Enrichment: Assessing and Model...
Studies: FAIR Functional Enrichment
Assays: FAIR Functional Enrichment