The Uniprot Free Text Search Interface

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Funiprotsequencefetcher.html;fp=help%2Fhtml%2Ffeatures%2Funiprotsequencefetcher.html;h=edd8995473b3aaa1242a208883947ce051267a10;hb=7d67fb613ec026dc9a265e351e7fab542e3f1d61;hp=9b2e3fa1da94cb2901545de25bd52d5d0a4666c0;hpb=02e38bb826828ab2991584cf4b737c0138cb6c44;p=jalview.git diff --git a/help/html/features/uniprotsequencefetcher.html b/help/html/features/uniprotsequencefetcher.html index 9b2e3fa..edd8995 100644 --- a/help/html/features/uniprotsequencefetcher.html +++ b/help/html/features/uniprotsequencefetcher.html @@ -20,142 +20,150 @@ * The Jalview Authors are detailed in the 'AUTHORS' file. --> -The Uniprot Free Text Search Interface +The UniProt Free Text Search Interface - The Uniprot Free Text Search Interface + The UniProt Free Text Search Interface +
Since version 2.10 (October 2016), the Jalview Desktop + provides a search interface for interactive discovery and retrieval of + sequence data from UniProt. This dialog enables UniProt sequence + metadata to be searched with free text and structured queries, which + allows sequences to be located via gene name, keywords, or even + via manual cross-referencing from UniProt or other + bioinformatics websites.

- Jalview provides a specialised interface that allows fast and - efficient discovery and retrieval of data from the Uniprot database. - It allows - interactive querying of Uniprot metadata with free text and structured - queries, so sequences can be located without prior knowledge of - their database accessions, or via manual cross-referencing - from Uniprot or other bioinformatics websites. + To open the UniProt Sequence Fetcher, select UniProt as the database + from any Sequence Fetcher dialog (opened + via "File →Fetch + Sequences").

- To open the UniProt Sequence Fetcher, select UniProt as the database from - any Sequence Fetcher dialog (opened via - "File →Fetch Sequences"). -

- Uniprot sequence fetcher (introduced in Jalview 2.9.1) +

- Searching the Uniprot Database + Searching the UniProt Database

- To search the Uniprot, begin typing in the text box. The results of your - query are shown in the search results tab, which queries Uniprot after 1.5secs every time - you type in the search text box. You can sort results according to - the displayed columns, and select entries with the mouse or - keyboard. Once you have selected one or more entries, hit the OK - button to retrieve and visualise the sequences in Jalview Alignment interface. + To search UniProt, simply begin typing in the text box. After a + short delay (about 1.5 seconds), results will be shown in the table + below. You can sort results by clicking on the displayed columns, + and select entries with the mouse or keyboard. Once you have + selected one or more entries, hit the OK button to + retrieve the sequences.

Searching a specific Uniprot field If you - want to find sequences based on a specific Uniprot metadata field, - you can select it from the drop-down menu.
Searching a specific UniProt field To + find sequences with particular UniProt metadata, you can select a + field to search from the drop-down menu.
Bulk UniProt record retrieval
To + retrieve several uniprot accessions at once, first select UniProt + ID from the dropdown menu, then paste in the accession IDs as a + semi-colon separated list. (e.g. fila_human; mnt_human; + mnt_mouse).
Hitting Return or OK will automatically fetch + those IDs, like the default Sequence Fetcher interface.
Bulk Uniprot retrieval
- Firstly, switch the search target to Uniprot Id, then enter multiple IDs by separating them with a semi-colon. - e.g. fila_human; mnt_human; mnt_mouse.
Hitting Return or OK will automatically - fetch those IDs, like the default Sequence Fetcher interface.

Advanced / Custom querying - The table below provides a brief overview of the supported Uniprot query syntax (see query fields for UniProtKB): - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

`human antigen`	All entries containing both terms.
`human AND antigen`
`human && antigen`
`"human antigen"`	All entries containing both terms in the exact order.
`human -antigen`	All entries containing the term `human` - but not `antigen`. -
`human NOT antigen`
`human ! antigen`
`human OR mouse`	All entries containing either term.
`human \|\| mouse`	All entries containing either term.
`antigen AND (human OR mouse)`	Using parentheses to override boolean precedence rules.
`anti*`	All entries containing terms starting with `anti`. - Asterisks can also be used at the beginning and within terms. Note: - Terms starting with an asterisk or a single letter followed by an - asterisk can slow down queries considerably. -
`author:Tiger*`	Citations that have an author whose name starts with `Tiger`. - To search in a specific field of a dataset, you must prefix your - search term with the field name and a colon. To discover what - fields can be queried explicitly, observe the query hints that are - shown after submitting a query or use the query builder (see - below). -
`length:[100 TO *]`	All entries with a sequence of at least 100 amino acids.
`citation:(author:Arai author:Chung)`	All entries with a publication that was coauthored by two - specific authors.

Complex queries + with the UniProt query Syntax The text box also allows complex + queries to be entered. The table below provides a brief overview + of the supported syntax (see query + fields for UniProtKB): + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

`human antigen`	All entries containing both terms.
`human AND antigen`
`human && antigen`
`"human antigen"`	All entries containing both terms in the exact order.
`human -antigen`	All entries containing the term `human` + but not `antigen`. +
`human NOT antigen`
`human ! antigen`
`human OR mouse`	All entries containing either term.
`human \|\| mouse`	All entries containing either term.
`antigen AND (human OR mouse)`	Using parentheses to override boolean precedence + rules.
`anti*`	All entries containing terms starting with `anti`. + Asterisks can also be used at the beginning and within + terms. Note: Terms starting with an + asterisk or a single letter followed by an asterisk can slow + down queries considerably. +
`author:Tiger*`	Citations that have an author whose name starts with + `Tiger`. To search in a specific field of a + dataset, you must prefix your search term with the field + name and a colon. To discover what fields can be queried + explicitly, observe the query hints that are shown after + submitting a query or use the query builder (see below). +
`length:[100 TO *]`	All entries with a sequence of at least 100 amino + acids.
`citation:(author:Arai author:Chung)`	All entries with a publication that was coauthored by + two specific authors.

Result pagination

- The query results returned from the Uniprot server are paginated for performance optimisation. - The button labelled ' << ' and ' >> ' can be used to navigate to the next or previous result page respectively. - The page range is shown on the title bar of the Free Text Search interface. Jalview's pagination implementation supports multiple selection of entries across multiple pages. - - -

- Customising The Uniprot Sequence Fetcher -

+ The query results returned from the UniProt server are paginated for + performance optimisation. The button labelled + ' << ' and + ' >> ' can be used to navigate to the + next or previous result page respectively. The page range is shown on + the title bar of the Free Text Search interface. Jalview's pagination + implementation supports multiple selection of entries across multiple + pages. + +

- To change the displayed meta-data in the search result, click the - 'Customise Displayed Options' tab, and select the fields you'd like - to displayed or remove. + Customising The UniProt Sequence Fetcher

To change the displayed meta-data in the search result, click + the 'Customise Displayed Options' tab, and select the fields you'd + like to be displayed or removed.

- The Uniprot Free Test Search Interface was introduced in - Jalview 2.9.1 + The UniProt Free Test Search Interface was introduced in + Jalview 2.10.0

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