LINCS Production Phase 2 Extended Metadata Standards
In LINCS Production Phase 2, the LINCS Data Working Group (DWG) is currently developing extended metadata specifications describing LINCS reagents, assays and experiments. Annotations for the perturbagens (small molecules, siRNA, growth factors and other ligands), cells, and some elements of experimental metadata should be common between all LINCS Centers. This will facilitate development of data analysis, formatting, and visualization strategies by LINCS investigators, and also the development of databases and data repositories in which to store and share LINCS data.
- Antibody reagents pdf xlsx (Released 5-13-16)
- Cell lines pdf xlsx (Released 5-13-16)
- Differentiated cells pdf xlsx (Released 5-13-16)
- Embryonic stem cells pdf xlsx (Released 5-13-16)
- iPSCs pdf xlsx (Released 5-13-16)
- Other reagents pdf xlsx (Released 5-13-16)
- Primary cells pdf xlsx (Released 5-13-16)
- Proteins pdf xlsx (Released 5-13-16)
- Small molecules pdf xlsx (Released 5-13-16)
Metadata required from the Data and Signature Generation Centers (DSGCs)
Each of the files listed below provides the canonical and batch required metadata that must be provided by each of the DSGCs.
- Antibody reagents pdf xlsx
- Cell lines pdf xlsx
- Differentiated cells pdf xlsx
- Embryonic stem cells pdf xlsx
- iPSCs pdf xlsx
- Other reagents pdf xlsx
- Primary cells pdf xlsx
- Proteins pdf xlsx
- Small molecules pdf xlsx
LINCS Pilot Phase 1 Metadata Standards
The documents below annotate reagents outside the context of the experiments in which they were used. For example, the small molecules standards do not include solvent information as that is usually specific to the experimental context in which the reagent is used. Please note that the ‘Unique ID’ field in these documents is used by the LINCS DWG to track fields and is not meant for any other purpose.
- Cell lines (Released 4-11-12)
- Primary cells (Released 4-11-12)
- Small molecules (Released 5-4-12)
- RNAi reagents (Released 7-31-12)
- Protein reagents (Released 7-31-12)
- Antibody reagents (Released 10-12-12)
- Other reagents (Released 11-7-12)
The LINCS DWG will also develop standards to annotate the metadata that should be reported to describe LINCS assay protocols, data analysis strategies, and datasets. As much as possible we plan to make use of experimental metadata standards developed by other groups such as the ISA infrastructure project, the MIBBI efforts (e.g. MIACA, MIARE), and NCBI PubChem.