Showing Category: ResNet Databases and Ontologies
How are contradictory relation findings resolved in Pathway Studio?
MedScan is a Natural Language Processing (NLP) tool that extracts facts from the literature. Extracted information is added in ResNet databases and can be...
How can I add proteins to a functional class?
You can add proteins to an existing functional class or a newly created functional class by doing the following:
1. Open a new pathway and add to the...
How confident am I in the accuracy of a relationship?
Usually the number of references which are associated with this relationship gives an indication of the accuracy of the relationship. As a rough guide,...
How do I export a pathway?
Select the file for export and select Export. A menu box appears with 3 export options. The first two options export the file as a *.gpp file that can...
How do I find the intersection between two groups?
You can find the intersection between two groups by doing the following:
1. Right-click on the first group icon in the explorer window and choose...
How do I find the intersection between two lists of groups?
Follow these steps to find the intersection between two lists of groups:
1. Open both list of groups in the list pane (ex. the results of a GSEA...
How do I find the subset of genes in an ontology group that identified in a GSEA analysis or a Fisher’s Exact test that are included in my experimental data list?
To find the overlap between the members of a group and the proteins in an experimental data set, do the following:
1. ...
How do I import a list of proteins?
In the database pane, select Import. From the drop-down menu select “Gene List”. The following dialog box appears (Figure 1).
Identifies such...
How do I see the reference information that supports a relationship?
You can see reference information for a relationship in a network diagram by placing the cursor over the relationship. A pop-up box will appear that will...
How often is ResNet Mammalian updated?
Currently this is done at 3 monthly intervals. You can download each quarterly ResNet update from the Ariadne website: www.ariadnegenomics.com. Log...
How often is the Gene Ontology updated?
Gene Ontology and Entrez Gene IDs are updated when major ResNet updates are released. Currently that is approximately once a year.
How often is the ResNet Plant database updated?
The ResNet Plant database is updated twice a year.
For more information about ResNet Plant 2.1 see the Technical Support Bulletin describing this database in...
How to Enable the Model Organism Cartridges in MedScan Reader 2.1 (or higher)
Previous to Pathway Studio 6.1, support for the knowledge recovery for model organisms, Drosophila, C.Elegans, and Yeast was “hardcoded” into the MedScan...
What are the full text journals included in ResNet 6.0?
What are the full text journals included in ResNet Plant 2.1?
1. Annals of Botany2. Crop Science3. Journal of Experimental Botany4. New Phytologist5. Plant Cell6. Plant, Cell and...
What is Ariadne Ontology?
Ariadne has prepared an organization of genes for use in interpretation of experimental data, simplification of pathway diagrams, and summarization of analysis...
What is Gene Ontology?
Gene Ontology is a controlled vocabulary (ontology) that describe gene products in terms of their associated:
biological processes;cellular...
What is the source of the cellular processes in ResNet?
The cellular process categories and associated aliases come directly from the Gene Ontology without further annotation or curation by Ariadne.
What is the source of the relationships in the ResNet Mammal databases?
ResNet 6 Mammalian includes molecular interactions, extracted by Ariadne’s MedScan (Natural Language Processing) technology, from over 17 million PubMed...
What is the source of the relationships in the ResNet Plant 2.1 database?
MedScan Dictionaries (Plant 2.1) are populated with all the gene symbols and aliases from Arabidopsis. When MedScan processes documents and encounters a...
