Version: 0.8.1

New Dataset

Supported by

EBI Databases Proteomics

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EnVision 2 Home

ABOUT EnVISION

In shortEnVision is a web interface to provide a summary of information for several services using protein Ids and protein sequences as input.

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License

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Acknowledgements

INPUT1

Select your input TYPE

Please provide a supported input for creating a new dataset. Valid input are 'Protein Accession' (UniProt IDs, IPI...) or 'Protein Sequences' (sequence only or in fasta format)
Envision needs at least one Protein identifier or Sequence to process a dataset.
Please write or paste your input into the input areaand make sure to select 'Accessions' when using protein accession numbers or select 'Protein Sequences' when using protein sequences in your dataset.

Mixed input (protein accession numbers and protein sequences) are not supported.

Here you can find a sample input for each input type.

Automatically created Datasets

For protein accession numbers please insert or past them in the input.
Use either a blank, a semicolon, a colon or a new line to space the accession numbers.
Do not forget to switch the input type option to Protein accession numbers.

Sample input:

In the sample above Envision 2 would split the input into the following five Accession numbers:

IPI00525929 (IPI Identifier)
P38398 (UniProt Identifier)
P14523 (UniProt Identifier)
T21552 (PIR Identifier)
NP_051052 (RefSeq Identifier)

for creating a new dataest.

To create a dataset from Protein Accession numbers you can either

Input the Protein IDs directly
Upload a file containing several Protein IDs
Provide the URL to a file with several Protein IDs

X	Protein AccessionsEnQuantProtein SequencesEnfin XML Document

Provide your input DATA

X	Direct InputFile UploadURL Load

Please input or paste various Protein Accession Numbers

SERVICES3

Chose a service workflow

Envision 2 uses predefined workflows to retrieve information about you input.
A workflow is predefined set of database queries (e.g. UniProt, Reactome...). It retrieves information about your input and stores it in a user friendly format. When all database queries are finished, the dataset becomes available for browsing.
If you do not change this option the default workflow will be run which is suitable for most users. If you wish to use another one select it. Information about you selection will be displayed next to the select box on the right side.

For more information about the provided workflows please go to the Workflow manual page or click here.

X

User input -> Protein Identifier Mapping

Protein Identifier Mapping -> Protein Identifications
Protein Identifier Mapping -> Protein Information
Protein Identifier Mapping -> Biological Pathways
Protein Identifier Mapping -> Molecular Interactions

X

Run services in parallel
This option will not include the 'Protein Mapping' service. It will create one dataset per service. Datasets can be merged in one EnXML file using the 'Dataset Manager' section.

Workflow options

Each workflow accesses several web services to fetch data and adds this to your dataset.

There are several options available to customize your dataset. To change them, please expand the web service and change the available options.
Some options can not be changed yet but will become available in the future.

MORE OPTIONS

Dataset name

To handle more than one request at a time Envision stores user input and results in datasets.
You can provide a name to better identify different dataset while working.
If you do not want to name a dataset the next default name starting with set1 (then set2...) will be used.

e.g. 'myDataset'

Limit by specie

You can limit your proteins to a certain species by using this option.
Proteins or protein interactions from other species will not be included in the datasets result.