Create annotation input

Version 11 (Patricia Sebastian, 05/31/2010 11:06 am) → Version 12/14 (Patricia Sebastian, 05/31/2010 12:05 pm)


h1. Create annotation Input Form

h2. Select your data

Here you can select the list of identifiers you want to convert. You should have uploaded it previously using the *[[upload_data_documentation|Upload Menu]]* in Babelomics and tagged it with the *idlist* data type. If you do not load any data, the tool uses all the genome as input data.

h2. Databases

- * *Organism*: Here you can select in a wide range of species your organism of interest.

- *Databases*: *[[Soft_ddbb_documentation|databases]]* available for the organism selected can be tested simultaneously and a specific filter option is provided for each one:

* *GO - biological process*:

> *GO parameters*</span>
> > +Select annotation through ontology levels+:
> > > ** Propagate Annotation to upper levels: GO terms are made up with the genes directly annotated to them and also the ones annotated in children GO terms.
> > > ** Direct Annotation: GO terms are made up with the genes that are directly annotated to them, without any inheritance rule applied.
> > +Select GO levels analysis+: range of selected levels of the ontology.

> *Filter terms by number of annotated ids in DB*.
> > Introduce a minimum and maximum number of annotated ids in the gene set to filter out smaller and bigger terms. The filter can be applied in all the genome or in the user input ids.

> *Filter terms by keywords*
> > Filter the database by one or more keywords, with the possibility of _and_ and _or_ boolean parameters. Only GO terms with a matching description to your criteria will be tested.
> > Add children of selected terms: the GO terms selected and its children are tested.

* *GO - molecular function*: you can define a filter with the same parameters as described above in _GO -biological process_ section.

* *GO - cellular component*: you can define a filter with the same parameters as described above in _GO -biological process_ section.

* *GOSlim GOA*
> *Filter terms by number of annotated ids in DB*.
> > Introduce a minimum and maximum number of annotated ids in the gene set to filter out smaller and bigger terms. The filter can be applied in all the genome or in the user input ids.

* *Interpro* motifs: you can define a filter with the same parameters as described above in _GOSlim GOA_ section.

* *KEGG pathways*:

> *Filter terms by number of annotated ids in DB*.
> > Introduce a minimum and maximum number of annotated ids in the gene set to filter out smaller and bigger terms. The filter can be applied in all the genome or in the user input ids.

> *Filter terms by keywords*
> > Filter the database by one or more keywords, with the possibility of _and_ and _or_ boolean parameters. Only GO terms with a matching description to your criteria will be tested.
> > Add children of selected terms: the GO terms selected and its children are tested.

* *Reactome*: you can define a filter with the same parameters as described above in _GOSlim GOA_ section.

* *BioCarta* you can define a filter with the same parameters as described above in _GOSlim GOA_ section.

* *MicroRNA*: you can define a filter with the same parameters as described above in _GOSlim GOA_ section.

* *Jaspar TFBS*: you can define a filter with the same parameters as described above in _GOSlim GOA_ section.

* *ORegAnno*: you can define a filter with the same parameters as described above in _GOSlim GOA_ section.</span> !!!! AquĆ­ falta

h2. Output format

Here you can select the format of your output data. You can choose one of these options:

* *Compact*: Each input identifier and its correspondences are grouped in the same line.
* *Extended*: An output correspondence per line. If an input identifier corresponds with more than one output identifier, each correspondence is showed in a different line.

h2. Job

* *Job name*. Give a short name to your analysis job
* *Job description*. You can use this section to document further the characteristics of this analysis

Its aim is to help you identifying the analysis you are running and distinguishing between several analysis.
To set the name is mandatory but you can leave the description empty if you do not want to use it.

h2. Run

Once all options are set you can run the job. You may get some *error* message if some parameters are not properly set. If you do, just check the options you have chosen.

See *[[Create_annotation_output|Output results]]* section for details on the result data format and plots.