How to query HoPaCI
- Per default the search space includes all types of data concerning pathogen-host relations.
- One can find interactions of the pathogen itself and interactions between pathogen and host. Queries are not case-sensitive and search all database content that includes the query term (e.g. flag is sufficient to find everything concerning flagella). This type of query is highly unspecific as it includes also information such as gene/protein name synonyms and authors names from referenced literature.
- The first box of the search options (Field) allows searching within a specific type of data, e.g. only within genes/proteins, biological processes etc. Per default, the search covers all fields.
- Combined queries can be performed by using Refine query. By clicking on Refine query a second search field is opened. A drop-down menu allows combining the two queries with the Boolean operators AND, OR and NOT.
- The search space can be restricted by setting the search term into double quotes (e.g. "type IV pilus" will not find type IV pilus-dependent motility which would happen without quotes)
- The character for wild-card is '%'. It can also be used in a double-quoted search term.
|cell death||Finds every term that contains the words 'cell' and 'death' anywhere (also synonyms!), i.e. you will retrieve 'cell death' and 'neutrophil apoptotic process'. The latter is a GO term that includes the words 'cell' and 'death' in the synonym of GO:0001781 : neutrophil apoptotic process (neutrophil programmed cell death by apoptosis).|
|"cell death"||Finds only exactly 'cell death' but not 'neutrophil apoptotic process'|
|%||Wildcard: Finds all interactions within the search space. If e.g. "all Fields" is chosen, all host-pathogen interactions of the database are shown. "cell%" finds every interaction with a term that begins with "cell".|
Visualization of data
- Pop-up windows show the information that is basis of the interactions
- Hovering over arrows/edges opens an info box with detailed information about the underlying interactions.
- Clicking on an arrow/edge results in opening new windows with the complete entry information, one for each entry.
- The thickness of an edge correlates with the number of interactions found for the same subject, object and interaction symbol.
- Moving objects/nodes
In order to move nodes (proteins, chemical compounds etc.) one first has to click on the yellow icon below the "Help" link.
Secondly, the user has to click on the respective node which in turn appears in darker colour. In this state, the node can be moved by using the left mouse button.
- Extending the graph for items of interest
Double clicking on an object (node) launches a new search extending the current information for all interactions that are associated with the respective node.
- Zooming and moving of the graph
For zooming the graph either the mouse wheel or the zoom function on the upper left of the graph can be used.
For moving the graph the left mouse button has to be hold down and the mouse to be dragged in the appropriate direction.
- Hide/show transitive interactions
Per default the graph not only shows the interactions of the search results but also interactions between the objects,
i.e. if a search finds a-b and a-c, a relation between b and c will also be shown, even if it is not found by your search.
If you do not want to see these relations click on the "Hide transitive relations" button on the lower left of the graph. To open them again click a second time on the same button.
- Graph download
Diagrams can be downloaded as SBML, graphML or jpg files by clicking on the respective buttons on the lower left of the window.
SBML: SBML files can be processed by numerous software tools (see SBML Software Guide). Instructive layout styles for Cytoscape users are e.g. yFiles organic, yFiles orthogonal, Cytoscape Force-Directed Layout, Cytoscape Spring Embedded and Cytoscape Edge-Weighted Force-Directed.
GraphML: Users that want to edit the graph should use the graphML format. The file can be opened and edited with the freely available yED software (http://www.yworks.com/en/products_yed_about.html)
Origin of the data
Data in HoPaCI are retrieved from research articles and also from reviews. All interactions are manually annotated by experienced biocurators and linked to the respective PubMed entries. For annotated genes, we provide links to EntreGene. These can be found in the interaction information list of the corresponding entries. The links are assigned as described below:
|P. aeruginosa||Gene names and IDs refer to strain PA14. For annotation of the gene names the database Pseudomonas Genome Database was also taken into account.|
|C. burnetii||Gene names and IDs refer to the type strain RSA 493.|
Curation of data
Information about pathogen-related interactions consists of three kinds of information.
- The central information is a structured interaction between two elements (e.g. protein A activates protein B). This is also known as subject-predicate-object structure. "Subjects" and "Objects" are linked/mapped to thesauri such as EntrezGene, KEGG, OMIM, miRBase, Gene Ontology, CORUM. The distinction of the genes referring to pathogen or host can be made by their notation.
- If a term is not available in these vocabularies, we introduce suitable terms.
- A textual comment allows to provide additional information about the experimental setup (e.g. concentration of a drug that was applied) and to present a more differentiated view than the structured information (e.g. the structured information is restricted to 'protein A increases_activity of protein B' whereas in the text we can specify that it is a 'significant' or a 'slight' increase of the protein activity).
- The general information consists of literature reference, organism, and if available tissue/cell line. All information is linked to the PubMed content of the respective journal articles.
Information in HoPaCI is given as entries and interactions. An entry comprises one or more result/-s (interactions) from one publication that was/were obtained under the same experimental conditions. An interaction is part of an entry and describes an interaction between two elements (e.g. protein A increases_activity of protein B).
Dr. Andreas Ruepp
Institute of Bioinformatics and Systems Biology/MIPS