PROMA is a proteome metadata annotator based on the OntoMaton tool. We have retained the original functionality of OntoMaton and added the ability to retrieve ontology and annotate the SDRF-Proteomics in Google Spreadsheet.

Function Introduction

PROMA is powered by the EBI Ontology Lookup Service, which greatly improves the efficiency of completing SDRF-Proteomics files.

The current version of PROMA has the following features:

• Insert a template: we provide 6 templates according to species classification, including cell-line, default, human, nonvertebrates, plants, and vertebrates. Note that each application of the template overwrites the first line of the current sheet.
• Insert related parameters: we organised the searched ontology information into the form of key-value pairs, with four parameters in total: modification parameters, instrument, cleavage agent details and label.
• Record: add a sheet named Record to record the parameter information searched and inserted.

Installation

To try PROMA, you need to add the extension to your Google spreadsheet. The following steps will make it easy.

1. Click on the 'Add-ons' menu item in your Google Spreadsheet:

SDRF Annotation

Select Template

If the properties of the first row have been correctly filled in, skip this step.

Select a template and click the "Apply" button. You should get the following results:

Annotate

We searched Ontology information through EBI Ontology Lookup Service, and sorted the label and obo_id in the returned information into the form of key-value pairs.When searching for modification parameters, we recommend modifying all parameters. To search for other types, just type NT or AC.

Click on the cell to specify the range, click on the "Insert" button in the search results, and you'll get something like this:

Record

When you insert, a 'Record' sheet will be added automatically. This sheet will have the following column headers: Parameter Type | Parameter Value | Term Name | Ontology Source | Term URI. This is how we record your inserts.

An example of a google spreadsheet with such functionality can be viewed here: https://docs.google.com/spreadsheets/d/1kg043sFW2-hkWD7u_0tT2KbG7d0HqftTkULo5kYvJrw/edit#gid=1680029552

Ontology Search

From Proma, you can only search one service within this tool: the EBI Ontology Lookup Service, and insert the terms in your Google Spreadsheet directly. Full term provenance is recorded for you and later downstream analysis.

Ontology Tagging

With Proma, you can select a number of spreadsheet cells and then 'tag' them. This means that OntoMaton will take the terms in the cells and send them to BioPortal's Annotator service. The results will come back as a list of the free text terms, showing for each all matches in BioPortal.

Configuring Proma - Settings

From the settings screen, you can configure:

• How terms should be inserted in to the spreadsheet when not in 'ISA mode' (where the next columns aren't named 'Term Source REF' or 'Term Source Accession'). The two options are as either as a hyperlink to the term in Bioportal/OLS/LOV or as a term name with the hyperlink in parentheses.
• Restrictions, which specify for zero or more columns (with a name in the first cell), restrictions that should be placed on the search space per each of the ontology lookup services we use (Bioportal/OLS) E.g. the column 'Label' is restricted to terms from the Chemincal Entities of Biomedical Interest ontology (ChEBI).

When you add a restriction using the 'Settings' panel for the first time, a 'Restrictions' sheet will be added automatically. This sheet will have the following column headers: Column Name | Ontology | Branch | Version | Ontology Name | Service. Then you may define for a particular column header in your spreadsheet what ontology should be searched (or list of ontologies) over what service (BioPortal or OLS). A restriction will only apply if using the corresponding service for search.

Additionally, within one ontology restriction, for BioPortal searches, you can restrict to a particular branch of an ontology, providing a way to further restrict the search space.

An example of a google spreadsheet with such functionality can be viewed here: https://docs.google.com/spreadsheet/ccc?key=0Al5WvYyk0zzmdDNLeEcxWHZJX042dS0taXJPNXpJMHc

Video Tutorial

Access the video tutorial showing how to install and use PROMA here.

Templates

PROMA templates are here.

Questions

For bug reports, please use the issue page here.

License