Introduction to 3M

LINCS 3M documentation focuses on creating data for the LINCS Knowledge Graph (KG). We recommend you review the official 3M manual for a general introduction to 3M and for in-depth information that is outside the scope of LINCS’s documentation. Community-made resources are also available.

The LINCS 3M instance comes preloaded with the ontology and generator files used for LINCS data conversion. To use the LINCS 3M instance, register for an account and wait for account approval from LINCS.

LINCS uses the 2022 version of 3M, and all screenshots are from this version. Although some external documentation contains screenshots from previous 3M versions, the information provided is still helpful.

3M Pages

This section gives an overview of the 3M pages you will use to convert data for publication with LINCS. It is not a comprehensive list of all the functions in 3M. More detailed instructions for 3M are available:

• The official 3M manual
• Creating a Mapping Project in 3M
• The Interface of a Mapping Project

Project Mappings

The Project Mappings page with annotations.

The Project Mappings page is the screen that loads after logging in. This is where you manage your conversion projects. We refer to the conversion rules you set up for each project as a mapping.

On the Project Mappings page, you can:

1. See all projects in the LINCS 3M instance
2. Organize your projects
3. Open your projects
4. Make new projects by
   1. Copying existing projects
   2. Creating new projects
   3. Uploading exported 3M ZIP files

warning

When using the LINCS 3M instance, your files will be stored on LINCS servers. We recommend that you regularly export your 3M projects and store them locally, as LINCS does not guarantee long-term storage for 3M projects. Exported projects can be re-uploaded to 3M. More details are available in Export & Extras

Files Metadata Management

Files Metadata Management window with annotations.

The Files Metadata Management window loads when you open a project. You can use this window to specify what data you want to convert and what ontologies the converted data should follow.

In the Files Metadata Management window you can:

1. Give a title to your source data input file (your XML file)
2. Change your source data input file
3. Add and remove Resource Description Framework Schema (RDFS) files for your chosen target schemas (ontologies)

Mappings Overview

Mappings Overview page with annotations.

The Mappings Overview page loads when you close the Files Metadata Management window. You can use the Mappings Overview page to set up the rules for converting your data.

On the Mappings Overview page you can:

1. Change the project
   1. Title
   2. Description
2. Change the view
   1. Expand or collapse all mappings
   2. Expand or collapse a single mapping
3. Import from an X3ML file
4. Export all mapping files as a ZIP file

Mappings Overview page with annotations.

For each mapping, you can also edit the:

1. Domain
2. Link
3. Source Nodes
4. Generators
5. Labels
6. Variables

Generator Definitions Manager

Mappings Overview page screen with Open Generator Definition Manager outlined.

You can access the Generator Definitions Manager by clicking Open Generator Definition Manager (link icon) in the top-right corner.

Generator Definitions Manager Dialog window with annotations.

The Generator Definitions Manager Dialog window lets you specify how you want to create entity labels and identifiers.

In the Generator Definitions Manager Dialog window you can:

1. Export definitions to a XML file
2. Use an existing generator file
3. Add new definitions to the project directly in the definitions manager
4. Delete existing definitions from your project

You can also edit generator definitions. For more information see Generators

“Produce RDF” (Transformed Output)

Mappings Overview page with Produce RDF outlined.

Transformed Output window with annotations.

At the bottom of the Mappings Overview page is the Produce RDF button. The mapping project is automatically saved in the LINCS 3M instance. To get your converted data out of 3M, you must produce RDF data.

On the Mappings Overview page and the Transformed Output window you can:

1. Change the RDF serialization (format) of the output
2. Download the output in your chosen format (RDF/XML, TTL, N-Triples, TriG)