This section of GenomeMine allows you to annotate your dataset according to the Genomic Metadata Exchange (GnoME) specification.
Step 1. Request a Life Science Identifier (LSID)
Note: We are in the process of establishing an LSID authority. Data can still be submitted to the database without an LSID and one will be supplied in the future.
(More information)
Step 2. Enter Provenance
Provide details of provenance (e.g. who generated it) for the dataset. Save resulting file locally.
Step 3. Define Variables
Upload your dataset as a tab-delimited spreadsheet and define dataset variables. Save resulting file locally.
Step 4. Submit your Data
Submit your files (provenance, definitions, and dataset in RDF format) to the GenomeMine database.
The Genomic Metadata Exchange (GnoME) Specification
GnoME is designed to capture the minimal amount of metadata required for a dataset to attribute proper credit to its authors and allow the dataset's regeneration.
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GnoME: Genomic Metadata Exchange
Pronunciation: 'nOm Function: noun
Etymology 1: Greek gnOmE, from gignOskein to know
Etymology 2: French, from New Latin gnomus 1: an ageless dwarf who [...] guards treasure
Definition sourced from Merriam-Webster OnLine
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Towards the publication of datasets that can be harvested electronically by LSID in a GRID computing context
Ideally it will be beneficial if curated and calculated data can be formatted in such a way that makes automated data harvesting possible. We are therefore working on the development of a generic file format for the capture and exchange of datasets describing complete genome sequences. In the future we hope to capture a rich enough set of metadata to allow any data set to be regenerated and properly credited. To do this, we propose to develop an LSID compliant file format using RDF that uses and extends the Dublin core to capture all associated metadata and data.
We are working towards a Genomic Metadata Exchange (GnoME) specification to capture 'row & column' data (spreadsheets).
Discussion Document
We are developing a discussion document with an overview of the specification that will be made available on this web site in the near future.
Submitting Annotated Datasets to the GenomeMine
This specification has been developed to allow the submission of published and unpublished data sets of genomic metadata to the GenomeMine database. The specification is designed to be rich enough to allow the automatic import of new datasets into the database where they can be viewed in several ways and downloaded.
Evaluate the Specification Online
An implementation of the GnoME Version 1.0 specification has been developed to provide an electronic way to annotate data sets to this standard. This interface can be used to evaluate the specification. Input forms can accept sandbox-style input for the sake of testing.
An Overview of the Annotation Process
For ease of use, the interface allows users to upload datasets in tab-delimited format and enter all annotations using plain text. The form will automatically transform the data and metadata into RDF and RDF schema files.