Spinal cord injury (SCI) is associated with complex pathophysiological processes that follow the primary traumatic event and determine the extent of secondary damage and functional recovery. Numerous reports have used global and hypothesis-driven approaches to identify protein changes that contribute to the overall pathology of SCI in an effort to identify potential therapeutic interventions. In this study, we use a semi-automatic annotation approach to detect terms referring to genes or proteins dysregulated in the SCI literature and develop a curated SCI interactome. Network analysis of the SCI interactome revealed the presence of a rich-club organization corresponding to a “powerhouse” of highly interacting hub-proteins. Studying the modular organization of the network have shown that rich-club proteins cluster into modules that are specifically enriched for biological processes that fall under the categories of cell death, inflammation, injury recognition and systems development. Pathway analysis of the interactome and the rich-club revealed high similarity indicating the role of the rich-club proteins as hubs of the most prominent pathways in disease pathophysiology and illustrating the centrality of pro-and anti-survival signal competition in the pathology of SCI. In addition, evaluation of centrality measures of single nodes within the rich-club have revealed that neuronal growth factor (NGF), caspase 3, and H-Ras are the most central nodes and potentially an interesting targets for therapy. Our integrative approach uncovers the molecular architecture of SCI interactome, and provide an essential resource for evaluating significant therapeutic candidates. — Zahraa Sabra 2015/07/03 02:32
This webpage provides the annotator tool used for abstract selection and term extraction in our paper entitled Molecular Architecture of Spinal Chord Injury with Protein Interaction Networks. In addition we provide a sample dataset of serialized abstracts on spinal cord injury. The tool was not tested with compatibility on non-Windows operating systems.
Below are the instructions to use the tool:
1. Download and unzip the file SAMNAToolAndData.zip . Notice that the file also contains open access third party libraries provided inside it for convenience. The file dependencies are listed under the project object model file pom.xml . Source code is also available src.zip
2. Run the jar file in the typical manner with your latest java runtime environment (jdk-1.8). A jar file compatible with jdk-1.7 is also available SAMNA-1.0.jar
3. Then select “Load Serialized Abstracts” button and choose the file “Spinal_Cord_Injury_Abstracts_04_02_14.xml.ser”.
4. Abstracts will be loaded automatically and terms will be highlighted in red and yellow colors. Terms can be removed or added through right click shortcuts.