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Export Data


Before converting your data, you need to prepare a version of it that is easy to share and work with. The idea is to export all of the data that you want to convert from your project’s data store and save it in a format suited for your next conversion step. Because this is a custom step for each project, relying on your unique data store, LINCS can only guide you on what the outcome should look like.

Resources Needed

If your data needs to be extracted from a data store like a relational database, you will likely need support from your database administrator. Support from a team member with basic programming knowledge (e.g., undergraduate Python experience) is useful for restructuring your data.

Research TeamOntology TeamConversion TeamStorage Team
Identify Source Data
Extract Source Data
Send Source Data

This step could range from a one hour task of downloading text files and moving them to a shared location, to a few days task of exporting complex relational data into XML files that group the relevant information.

Identify Source Data

The Research Team identifies which dataset or part of a dataset they hope to convert. You will need to work with your technical team to answer:

  • Where is the data stored?
  • How can you access it?
  • Whose help do you need to access it? To export it? To restructure it?

Many projects have their data available to view on a website. When we talk about exporting data, we mean that you need to find out where the data is actually stored—where is the website getting the data from? You will need to go straight to that source or identify that there is an API or a data download link that can handle the export for you.


If you plan to contribute your data to LINCS, your Research Team, the Ontology Team, and the Conversion Team will meet to discuss the structure and contents of the identified dataset. We will discuss the overarching research goals of the Research Team so LINCS can create Linked Open Data (LOD) that is useful and meaningful.

It is helpful for the Research Team to come to this meeting prepared with some research questions they are hoping to answer.

Expected Outputs

The expected output depends on the structure of your data and the conversion tools you plan to use. It is helpful to review the rest of the conversion workflow steps before completing this step, particularly the Implement Conceptual Mapping step.

If you plan to use 3M for conversion, as LINCS typically does for structured data, then export the data and transform it into XML document(s) following the suggestions in Preparing Data for 3M.

Otherwise, you can:

See the Implement Conceptual Mapping page for help deciding if 3M or a custom solution is right for your data.

Send Source Data to LINCS

For LINCS to provide guidance as you convert your data, we need to see the data.

If the data is publicly available on a website or through an API, then please share links and documentation. This documentation helps us see the meaning that you are showing through the data.

We also need a copy or sample of the exported data that you prepared based on this page so that we can understand your technical needs.