Table 2.
Operational Characteristics of Stem Cell Databases
| Database | Search Features | Storage Platform and Interface | Privileges Needed for Access | Update Methodology | Current Status |
|---|---|---|---|---|---|
| SyStemCell | - Browse by organism, level of regulation, stem cell type, or control sample | - Stored in MySQL relational database and configured on RedHat Linux Server | Free access | Not specified | No longer available |
| - Search by Gene Entrez ID, gene symbol, or gene alias | - Web interface implemented on an Apache server | ||||
| - Online analysis tools developed in R | |||||
| CODEX | - Browse by cell type, repository, transcription factor, histones and associated proteins, or sequencing platform | - Not specified | Free access | Self-developed web crawler which constantly searches GEO database | Still available, unclear if still being updated |
| - Search by transcription factor, gene, or cell type | |||||
| ESTOOLS Data@Hand | - Can search by any annotation parameter: organism, cell type, disease state, etc. | - Stored in MySQL relational database | Free access with registration | Manually updated four times per year | No longer available |
| - Web interface implemented on Apache server | |||||
| Stem Cell Discovery Engine | - Search by free text, organism, measurement, technology, or platform | - Implemented on Harvard’s custom Galaxy server system | Free with registration | Researchers submit experiments which are then manually curated | Still available but has been merged into Harvard’s Stem Cell Commons data repository |
| StemFormatics | - Search by gene, species, author, platform, or cell type | - Not specified | Free access but registration needed to access certain features | Manually updated | Still active and available |
| LINCS | - Search by datasets, small molecules, or cells via any annotation | - Stored in PostgreSQL database | Free access | Data is submitted and uploaded via the LINCS Data Registry protocol | Still active but all features not yet available |
| - Free text search of all data with Boolean logic integration | - Web interface implemented using Apache Solr | ||||
| - Search by chemical structure by uploading mol files | |||||
| LifeMap Discovery | - Search by organ/tissue, cell type, related cell therapies, or gene expression | - Not specified | Free access but registration needed for access to all features | Not specified | Still active and available |
| StemMapper | - Search by tissue, cell type, and gene | - Stored in MySQL relational database | Free access | Not specified | Still active and available |
| - Web interface implemented using JavaScript ad JavaServer Faces 2.1 | |||||
| ESCAPE | - Browse by data type | - Stored in MySQL relational database | Free access | Not specified | Still available |
| - Search by gene name, gene ID, cell type, PubMed ID, or submission date | - Displayed via Cytoscape web plugin | ||||
| - Web interface implemented on Apache server and Java server | |||||
| SKiP Stem Cell Knowledge and Information Portal | - Search by associated disease, cell type, tissue type, disease status, donor characteristics, vector, database, PubMed ID, or text search | Not specified | Free access | Not specified | Still available but last updated in 2017 |
| hPSCreg | - Search by country, date, PubMedID, disease, cell type, or free text search | Not specified | Free access but registration needed for access to all features | Not specified | Still active and available |
| CellNet | - Browse by organism | - Online analysis tool developer in R | Free access | Not specified | Computational platform is available |
| - Search by cell deriviation, transcriptional targets, gene regulatory | - Affy packages by Bioconductor need to be installed | ||||
| -Review targets, gene regulatory network of starting cell type, gene expression | - Web interface implemented using JavaScript and JavaServer Faces 2.1 | ||||
| StemCellNet | - Browse by organism | - Not specified | Free access | Not specified | Still available versitile platform |
| - Search by proteins, transcription factors, genes | |||||
| HSC-explorer | - Browse by Gene, protein, SNP, biological process, cellular component, tissue, cell line, organism, chemical compound | - Not specified | Free access | Manually curated | The platform is expanded to cover all hematopoietic progenitors |
| ‘- Search by entry ID, Pubmed ID, comment, author, etc. | |||||
| CORTECON | - View by gene, disease, KEGG pathway, GO ontology | - Not specified | Free access | Not specified | Available for download |
| - Provides tools for browsing genes, expressed during cortical development | |||||
| ESCD | - Browse by Ensembl gene IDs and gene names | ||||
| - Browse by organism, transcription factors, GO terminology | - Not specified | Free access | Not specified | Datasets originate from genome version platforms |