Gut Cell Atlas logo

Gut Cell Atlas

Following on from the Chan Zuckerberg Initiative funded project, this Helmseley Charitiable Trust funded project is part of the Helmsley Trust's Crohn's Disease Program. More details of the funding can be found at

The goal of this project is to provide an integrated dataset of single-cell gene expression data mapped onto a high-resolution 3-dimensional framework from intestines (terminal ileum and ascending colon) of healthy individuals and Crohn’s disease patients undergoing resection due to intestinal obstruction or stricturing disease. This grant will also provide a gut-centric coordinate framework to map anatomical locations of cells providing novel insights into Crohn’s disease mechanisms, crucial to developing personalized therapeutic strategies, and new analytical tools for querying the Gut Cell Atlas database.

BISEL will be joined in this project by a team from the Pathology Division of the University of Edinburgh (led by Prof Mark Arends) and the EBI's Papatheodorou team with the Sanger Centre's Adams Group plus an NHS team led by Shahida Din.

Past projects

CZI logo

Comparative Workbench

A Chan Zuckerberg Initiative funded project exploring the spatial description of pathological annotations on the digestive system.

This is funded as part of the Chan Zuckerberg Initiative's pledge to support the development of the Human Cell Atlas.

The project will build upon research undertaken in PhenoImageShare and published here.

BISEL will be joined in this project by a team from the Pathology Division of the University of Edinburgh, led by Prof Mark Arends.

PHIS logo


A BBSRC project exploring the sharing of annotations on phenotype images.

For more information click here.



Combining and Uniting Business Intelligence with Semantic Technologies.

For more information, click here.

Argudas logo


Focused on the study and design of a multiscale ontological framework in support of the Virtual Physiological Human community to improve the interoperability amongst its Data and Modelling resources.

For more information click here.

Argudas logo


Arguing about inconsistent and incomplete information within a biological resources.

For more information click here.

Sealife logo


A Semantic Web browser for the life sciences.

For more information click here.



An EU Network of Excellence with the goal of establishing Europe as a leader in reasoning languages for the Web.

For more information click here.

XSPAN logo


Supporting cross-species access to tissue-based genetic information through the development of an internet-based cross-species anatomy network.

For more information click here.

© 2005- BISEL, School of Mathematical and Computer Sciences, Heriot-Watt University, Edinburgh, Scotland.