User manual, GOTaxExplorer, Version 1.0

Query language

The query language provides support for four basic query types.

Selection of sets
```
  <result> WHERE <condition> RESTRICT <limit> GROUP <go groups>
  
```
This query allows for selecting user-defined sets of entities from one of the data sources.
Comparison of Pfam sets
```
  PFAM WHERE <condition> PFAMCP PFAM WHERE <condition>
```
This query allows for comparing two user-defined sets of Pfam families with each other. The results are shown in the map of the Pfam functional space as defined in the paper (Schlicker et al., BMC Bioinformatics, 2006 Jun 15;7(1):302).
Comparison of GO sets
```
  GO WHERE <condition> RESTRICT <limit>
    SIM GO WHERE <condition> RESTRICT <limit>
```
This query performs a semantic comparison of two user-defined sets of GO terms. For each GO term in the first set, the functionally most similar term in the second set is reported.
Computation of functional equivalents
```
  GENE WHERE <condition> FUNSIM GENE WHERE <condition>
```
This allows for functionally comparing proteins according to their GO annotation.

Result

The <result> can be composed of one or more of the following types: GO, PFAM, SMART, TAX, LTAX, GENE. Different results have to be separated with a comma ",". LTAX returns the lowest common taxon in the taxonomic tree that satisfies a given condition.

Condition

The condition is composed of boolean operators and entity definitions. The operators "AND", "OR" and "NOT" are available. Round brackets "(...)" can be used to group parts of the condition. An entity is always defined with a keyword that indicates the data source followed by a colon ":" and the accession number from the source database, e.g. "GO:GO:0000015" or "PFAM:PF02811". It is possible to use an asterisk as wildcard for all entities of a specific type, e.g. "SMART:*" for all SMART domains. The following keywords are defined:

GO
for GO terms. Select entities that are annotated with this GO term. Note: The accession number of a GO term usually consists of "GO:" and 7 numbers. Therefore, the full entity has the form GO:GO:xxxxxxx!
DGO
for GO terms but use the smart2go or pfam2go mappings; this is only possible for SMART and PFAM results.
PGO
for GO terms. Select entities that are annotated with this GO term or any of the GO terms predecessors in the GO graph.
SGO
for GO terms. Select entities that are annotated with this GO term or any of the GO terms successors in the GO graph.
PFAM
for PFAM families.
DPFAM
for PFAM families but use the pfam2go mapping for GO results.
SMART
for SMART domains.
DSMART
for SMART domains but use the smart2go mapping for GO results.
TAX
for a taxonomic group or species; each species in the group is resolved to a set of result entities and the final result is calculated as the union of these sets. Therefore, all entities are selected that appear in at least one of the species belonging to this taxon.
ATAX
for a taxonomic group or species; each species in the group is resolved to a set of result entities and the final result is calculated as the intersection of these sets. Therefore, only entities are selected that appear in all species belonging to this taxon.
GENE
for a protein.
RESULT
Use the result from one of the previous queries in the current query. This allows to further refine results. One result is specified by a number starting with 1, e.g. RESULT:6 for the sixth result tab in the current result frame. Already deleted results cannot be used with this keyword.

Limit

Limits are only applicable to GO and taxonomy results. They are ignored in all other cases. The taxonomy queries can be limited to return only species by adding "SPECIES" to the <limit>. GO results can be limited to ontologies using "TT:ontology". Here, "ontology" can either be "biological_process", "molecular_function" or "cellular_component". Adding "EXTT" to the <limit> leads to the exclusion of the specified ontologies. Similar to this, it is possible to restrict the results to mappings with selected evidence codes. The codes are added with "EC:ec" where "ec" is a valid evidence code. The specified evidence codes can be excluded from the computation by adding "EXEC" to <limit>.

Group

Grouping is only applicable to GO results. The keyword is ignored in other cases. The number of GO terms satisfying the query and being a descendant of is calculated for the terms in the list after the GROUP keyword. The results are summarized in a table in the Results frame and visualized as histogram in a new window.

Sample queries

A query that selects all human proteins is


  GENE WHERE TAX:9606

A more complex query that selects all species with proteins belonging to the PHP domain (Pfam accession: PF02811) and involved in "DNA repair" (GO:0006281) reads


  TAX WHERE PFAM:PF02811 AND GO:GO:0006281 RESTRICT SPECIES

The query


  GO WHERE TAX:4751 RESTRICT TT:biological_process
    SIM GO WHERE TAX:9606 RESTRICT TT:biological_process

compares all GO biological process from fungi (Taxonomy accession: 4751) with the processes from human (Taxonomy accession: 9606). Modifying the query to compare only processes from fungi that are not in human leads to


  GO WHERE TAX:4751 AND NOT TAX:9606 RESTRICT 
  TT:biological_process SIM GO WHERE TAX:9606 
  RESTRICT TT:biological_process

Performing a functional equivalence comparison between Mycobacterium paratuberculosis and human is possible with the following query


  GENE WHERE TAX:1770 FUNSIM GENE WHERE TAX:9606