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.

Examples:

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".