CTSC:TTIC.032409

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Agenda

1. Introduction of Dr Yong Gao, XNAT engineer
2. Imaging consultations (Dr Dodson, lingual nerve, Dr Freedman, imaging of inflammation and Dr Lahav, creation of neonatal-MRI team)
3. Introduction by Gordon Williams of Dr Marie Gerhard-Herman, Director of the non-invasive vascular laboratory at BWH
4. Update onXNAT-i2b2-PACS integration project
5. Creation of a pilot grant fund for scanning
6. Recommendation for the IRAT/CTSA Baltimore meeting March 29-31

Harvard Translational Imaging Consortium Meeting Minutes March 17, 2009

In attendance:

• Gordon Williams
• Randy Gollub
• Gordon Harris
• Bill Hanlon
• Valerie Humblet
• Stephan Voss
• Bob Lenkinski
• Simon Warfield
• Yong Gao
• Sarah McMordie
• Annick Van den Abbeele

1. Presentation of Dr Yong Gao

• Dr Yong Gao is joining the Imaging Consortium as the computational engineer in charge of the XNAT-PACS-i2b2 integration project. Below is a description of his current research interest.
  • Neuroimaging techniques such as MRI, fMRI and PET provide a wealth of quantitative information related to anatomy, function, development, and disease etiology of the nervous system. Experimental studies utilizing neuroimaging techniques have generated and reported growing amount of research results in the literature. The availability of these results allows neuroscience researchers to perform comparative and integrative studies to discover new knowledge and generate new hypotheses. However, because that much of these results are published in the full text body of the articles as tables and figures, in addition to the textural format, they are not readily available for systematic retrieval and access via most online databases of scientific literature, such as PubMed, that cover only the abstracts and citations. To address this problem, we have developed the Internet Brain Volume Database (IBVD), a web-based searchable database of neuroanatomic volumetric observations manually curated from the journal articles. However, it is becoming apparent that our current labor-intensive manual approach is inadequate to keep pace with the growing number of publications. We propose to automate the development of IBVD with information extraction (IE) techniques. The primary long-term goal of this project is to develop a software system called NeuroIE that automatically search, extract, integrate and share research results from the published neuroimaging articles. The specific aims of the proposal are: (1) Identifying and develop volumetric neuroimaging domain lexicon and ontology. Ontological structures specific to the volumetric neuroimaging domain will provide both guidance and constraints for analyzing tables, document structure and English sentences, as well as the intermediate framework for representing the extracted knowledge. The ontology will also link to the volumetric neuroimaging lexicon that provides necessary vocabulary for language processing. (2) Developing NeuroIE’s core information extraction component. NeuroIE will be able to extract the following neuroimaging study results from full text of published journal articles: demographic information of subjects, volumetric measurements, disease diagnosis, and the neuroimaging methods used in the study. (3) Integrating NeuroIE with IBVD. By focusing on the neuroanatomic volumetric observations, the NeuroIE project will develop algorithms and software for mining the neuroimaging studies from the published literature, resulting in automated process of acquiring and entering data for neuroimaging databases, in support of advancements in understanding the underlying neuroscience in health and disease.

2. Consultation requests submitted through the Catalyst website

• Valerie gave the group an update on two on-going imaging consultations and information on a new one.
  • The group reviewed the new consultation and came with a series of suggestions for the investigator.
  • Valerie will do the follow-up and put the investigator in contact with experts in his domain.

3. Introduction by Gordon Williams of Dr Marie Gerhard-Herman, Director of the non-invasive vascular laboratory at BWH

• Dr Gerhard-Herman will be joining the Imaging Consortium next week. She will bring expertise in ultrasound and cardiovascular imaging.
• The team is also looking to add a second cardiovascular expert. Bob is in charge of recruiting an expert at BIDMC.
• In the future if the number of consultation requests about cardiovascular imaging increases significantly, the team will recruit experts from MGH or Children's as well.

4. Update onXNAT-i2b2-PACS integration project

• The members involved in this project have a meeting on Friday March 27 with Dr Dan Nigrin, Chief Information Officer at Children's Hospital.
  • Members who can not attend the meeting are invited to send their comments to Valerie or Randy who will send a summary to the group later this week.
• A problem for some researchers is the accessibility to PACS data, especially PET data. The issue will be discussed on Friday.
• Another subject of interest is the integration of the PACS-XNAT system with i2b2.
• Stephan presented the Childhood Cancer Grid which could potentially provide a backbone to facilitate inter-institutional data transfer. Two servers have been installed so far: one at Children's and one at the Dana Farber. The Director of this effort is Stephan Erberich, and he is based at USC. It will also be discussed at Friday's meeting.

5. Creation of a pilot grant fund for scanning

• A couple of members have agreed to meet with Gordon Williams to come up with a proposal for small pilot grants for imaging scans to able investigators to get some preliminary data in order to submit a grant to NIH or other institution.
  • The Consortium agreed that teaming with the Genetics Consortium and write a proposal for a single approach.
  • If this system of funding is approved, it will require a review board that can expedite the process.
  • The proposal must be ready before the end of April when Gordon will present it to Catalyst Central.

6. Recommendation for the IRAT/CTSA Baltimore meeting March 29-31

• The Baltimore meeting provides the opportunity for the Imaging Consortium to share with the rest of the National CTSA its expertise. We are a pilot for what CTSA hopes to do: interconnect the different CTSA a a national level. It is basically what we are doing intra-Harvard.