Difference between revisions of "FlyBase:QuickSearch"

Revision as of 19:37, 9 March 2016

General help

Overview

The QuickSearch tool on the FlyBase home page allows searching across all FlyBase reports. Forms for searching specific types of data have been separated into ‘tabs’, arrayed at the top of the QuickSearch window. Several of the tabs contain entirely new search tools, such as a new ‘Simple’ search form, an easy–to–use tool with access to all the data types in FlyBase. More information on how to use QuickSearch can be found below.

Links to specific help for each tab:

Species Searched

Several tabs search data that may be species-specific. In these tabs, a Species checkbox appears giving you the option to ‘include non-Dmel species’ in your search results. The default behavior is to return only Drosophila melanogaster (Dmel) data.

In the Data Type tab, an override behavior is available. To search for data in a non-Dmel species you can add a 4-letter species prefix to the symbol you are using to search, separated by a backslash (‘\’). For example, if you type Dvir\dpp, the search results for the gene symbol dpp will be filtered for those associated with D. virilis only.

Controlled Vocabularies

Several QuickSearch tabs search FlyBase data by making use of controlled vocabulary (CV) terms. These tabs provide intuitive domain-specific searches of FlyBase reports based on the Gene Ontology (GO) controlled vocabulary, on anatomical, developmental-stage-specific or phenotypic class terms used to annotate phenotypes, and on anatomical and/or developmental-stage-specific terms used to annotate gene expression. Combinations of CV terms can be searched using the forms in these tabs. An auto-completion feature is active wherever a search term should come from a CV, to assist you in choosing terms that will match records in FlyBase.

Auto-completion

The QuickSearch auto-completion feature is active in tabs that search FlyBase using controlled Vocabulary terms. Since only terms that are in the controlled Vocabulary will match records in FlyBase, the auto-completion feature suggests CV terms that are compatible with what you have typed. Selecting a term from the suggestion list reduces the possibility of a search returning nothing because the search term is not one that is used by FlyBase curators.

Some tabs for non-CV-based searches also use the auto-complete feature. Several of the searchable fields available in the References tab are enhanced with auto-completion, which helps prevent searches that fail due to mis-spelled names or mis-remembered journal titles. Most of the data classes searchable under the Data Type tab have auto-completion associated with them as well.

The QuickSearch auto-completion feature overrides your browser’s auto-completion function.

Coordinated Auto-completion

The coordinated auto-completion feature is active for tabs in which several search terms may be used simultaneously for a search. When a term has been entered in one of these fields, the coordinated auto-completion for the other fields is aware of the term already typed, and suggests only terms that actually occur in combination with the first term in FlyBase reports. Here is an example of how it works in the Expression tab:

When the expression pattern (lit. curated) data class is selected, text box fields for Stage, Tissue, and Cell Loc. (cell location) are displayed. The auto-completion for these three fields is coordinated in the following sense: Suppose you enter "fertilized egg stage" in the Stage text box. When you move your focus to the Tissue text box, auto-complete there will show only four options; "egg", "female pronucleus", "fertilized egg", and "male pronucleus". This is because, out of the multitude of CV terms available for the Tissue field, only these four terms have actually been used in combination with "fertilized egg stage" by curators in an annotation captured in the FlyBase database. If you enter any other term in the Tissue text box, even though it may be a valid CV term for that field, your search would return zero hits, because there are no FlyBase reports containing that combination of CV terms.

Using the terms suggested by the auto-completion feature ensures that you do not enter terms that would be mutually exclusive (or are simply not used by curators) in FlyBase reports. Terms suggested by the auto-completion should always return results. If the coordinated auto-completion does not offer a term you wish to enter in a field, it is because this term does not appear in combination with some other term you have entered elsewhere on the form. In this case you should try another combination.

Wild Cards

When you use QuickSearch you can add the asterisk character ( * ) to the beginning or the end of a search term. This is recognized as a “wild card” and will find all terms that contain your search term at the end or beginning of a phrase, respectively. You can also flank your search term with wild card characters to find all phrases containing your search term. For example, you can find the genes that start with 'ft' by entering 'ft*'. (Search the Genes data class either under the Simple tab by selecting the 'Genes' data class from the result summary table, or under the Data Type tab by selecting 'genes' from the Data Class drop-down menu.) The result of this search lists fat (ft) and fushi tarazu (ftz), as you would expect, and also fruitless (fru), because it has the synonym 'fty'.

Tab Descriptions

Simple tab

This tab performs a comprehensive search of text-searchable FlyBase data. This includes most fields from sixteen data classes of reports. The search returns a result page summarizing the matching records by data type. Clicking on one of these data types takes you to a secondary result page containing a table of individual matches within that data type. QuickSearch also places your query text in a resubmission form on the result summary page, where you can edit or refine the phrase directly and search again, without having to start over.

The QuickSearch auto-completion feature is not active in this tab.

Data Class tab

This tab contains a subset of the previous version of QuickSearch, and is laid out with very little change from that version. The Data Class drop-down menu restricts searches to only the single data type chosen, as before.

The QuickSearch auto-completion feature is active for most of the data classes in this tab.

Expression tab

Search for genes according to expression patterns:

At the top of this tab is a link to the RNA-Seq Profile Search tool. This tool can be used to search for genes by specifying a pattern of expression, as evidenced by high-throughput RNA-seq experiments.

Use the form below this link to search curated statements that describe published accounts of transcript and polypeptide expression. The input form has input boxes for developmental Stage, body part or Tissue, and subcellular localization (Cell Loc.). The coordinated auto-completion feature will assist you in finding the appropriate controlled vocabulary (CV) terms that have been used during the curation of each descriptor.

You can refine this search further by choosing to add qualifier terms. The coordinated auto-completion feature will provide you with a list of CV terms that have been used by curators to modify or limit the associated main term. The auto-completion for the qualifier terms is fully coordinated across all of these fields, in the sense that choosing a term for (e.g.) the Stage input will affect which qualifier terms are suggested for the Tissue or Cell Loc qualifier fields.

Phenotype tab

Search for alleles that have particular phenotypes. The form is divided into two portions, which may be used independently or in combination. The coordinated auto-completion feature will assist you in finding the appropriate controlled vocabulary (CV) terms that have been used during the curation of each phenotype.

The top section searches for alleles with a particular phenotypic class, e.g. "lethal" or "behavior defective". You can refine this search further using the refinement boxes, searching for a phenotype that occurs at a particular developmental stage, e.g. an embryonic stage and/or under particular conditions, e.g. "recessive" or "heat sensitive".

The bottom section searches for alleles that show a phenotype in a particular tissue or cell type, e.g. "wing" or "RP2 neuron". In this case, terms from the controlled vocabulary or cellular component terms from the Gene Ontology controlled vocabulary are used. Again, you can refine this search further using the refinement boxes.

Please note that the coordinated auto-completion works within the two sections, but not between them. This means it is possible even when using auto-completion suggestions, to search on a combination of terms entered in both sections of this form that will return zero hits.

References tab

This tab searches the extensive FlyBase bibliography. Searches can be filtered by title/abstract text, journal name, publication type, and reference IDs (PubMed or FlyBase), in addition to the author and date filters. Appropriate fields also allow the use of Boolean operators, so you can search for papers authored by e.g. “Smith NOT Johnson”. In addition to Boolean operators the year field supports mathematical comparison symbols (>,>=,<,<=) and range indicators (-,--,..). For example,

>2003 <=1945 1999-2003 1970-1990 NOT 1976 1992 OR 1995 OR 1998 The QuickSearch auto-completion feature is active for the fields in this tab where it will be helpful, such as the journal name field. These fields are indicated with a superscript.

GO tab

Search the Gene Ontology (GO) controlled vocabulary directly. Results are a CV term report, or list of reports. Once you are looking at the term report, you can then get a list of genes that are annotated with that GO term (look in the Records annotated with this exact term section), among other things. Please see the CV term report help page for more information.

The QuickSearch auto-completion feature is active in this tab.

Protein Domains tab

Search using InterPro IDs or signatures, including protein domains, families, repeats, and sites.

Either start typing and select a term from the drop-down menu, or enter your own search term using wildcard(s) (*) if desired. Resulting hits will be genes whose protein products are annotated with an InterPro signature that wholly or partially matches your term. N.B. Search with an InterPro ID (e.g. 'IPR019956') if you wish to retrieve hits annotated with a specific InterPro signature.

See the InterPro [FAQ] page for an explanation of these different signature types.

The QuickSearch auto-completion feature is active in this tab.

Gene Groups tab

Search the FlyBase-curated Gene Group data class using a gene or Gene Group symbol, name, synonym or ID.

The QuickSearch auto-completion feature is active in this tab.

Click the 'Browse' button to see a full list of Gene Groups.

Human Disease tab

Search the Disease Ontology (DO) controlled vocabulary to find alleles that have been used as disease models. Enter the name of a disease into the search box. The results are a list of Disease Ontology CV reports that match the inputted term. From the CV report you can get a list of all genes or alleles that have been used to model, or interact with a model, of that disease in flies. Please see the CV term report help page for more information.

The QuickSearch auto-completion feature is active in this tab.

Orthology tab

This tab can be used to quickly search for orthologs of D. melanogaster, human or other model organism genes, as provided by the DRSC Integrative Ortholog Prediction Tool (DIOPT) or OrthoDB. The DIOPT dataset integrates ortholog predictions for 8 model organisms from multiple tools and algorithms. (Further documentation is here.) The OrthoDB dataset (as implemented in FlyBase) comprises ~40 species, biased towards those that are closely related to D. melanogaster, and arranged into 5 ‘orthology groups’.

To use, first select the input species by clicking on the Species drop-down menu. Next, enter one or more gene symbols/IDs in the adjacent Gene(s) box - multiple entries need to be separated by spaces. Then, select one or more output species using the check-boxes - where the input species is D. melanogaster, there is a choice between searching the DIOPT or OrthoDB datasets. Finally, click the green Search button or press ‘enter’.

If the input species is D. melanogaster, then FlyBase gene symbols (e.g. ‘park’), annotation symbols (e.g. ‘CG10523’) or gene IDs (e.g. ‘FBgn0041100’) can be entered in the Gene(s) box. For other species, model organism database symbols (e.g. ’PARK2’) or IDs (e.g. ‘HGNC:8607’), or NCBI Gene IDs (e.g. ‘5071’) or Ensembl IDs (e.g. ‘ENSG00000185345’) can be entered. Note that symbol-based searches are case-sensitive - to ensure validity, users should select a gene symbol from the auto-suggest list that appears while typing. This tool does not support searching using gene fullnames.

On the results page, the top row shows the search term, species, the matched gene symbol, and any relevant links. Below this are the column headers, followed by the list of ortholog predictions arranged by species. For DIOPT-based searches, the columns are:

Ortholog Gene: official gene symbol, as used in model organism database
Ortholog Gene Reports: links to report pages at model organism databases, NCBI, Ensembl and/or OMIM
Score: a simple score indicating the number of tools that support a given orthologous gene-pair relationship
Best Score: either ‘yes’ or ‘no’ to indicate whether the given ortholog has the highest score for the query gene
Best Rev Score: either ‘yes’ or ‘no’ to indicate whether the query gene has the highest score for the given ortholog in the reciprocal search
Align: link to an alignment between the given orthologous gene-pairs on the DIOPT site
Source: list of individual ortholog prediction tools that support a given orthologous gene-pair relationship
Transgene in Fly: link to a FlyBase Gene Report for a non-Drosophila gene, indicating that that gene has been expressed transgenically in Drosophila

The results page is similar for OrthoDB-based searches, except that the DIOPT-specific columns are removed and the ‘Source’ column lists only ‘OrthoDB’.

In cases where there are multiple hits to a single search term (as may happen when a numerical ID is entered), then all hits together with their predicted orthologs are shown in the results table.

Difference between revisions of "FlyBase:QuickSearch"

Revision as of 19:37, 9 March 2016

Contents

General help

Overview

Species Searched

Controlled Vocabularies

Auto-completion

Wild Cards

Tab Descriptions

Simple tab

Data Class tab

Expression tab

Phenotype tab

References tab

GO tab

Protein Domains tab

Gene Groups tab

Human Disease tab

Orthology tab

Navigation menu

Search

@@ Line 3: / Line 3: @@
 ===Overview===
-The QuickSearch tool on the FlyBase home page allows searching across all FlyBase reports. Forms for searching specific types of data have been separated into ‘tabs’, arrayed at the top of the QuickSearch window. Information on how to use each of the QuickSearch tabs can be found below.
+The QuickSearch tool on the FlyBase home page allows searching across all FlyBase reports. Forms for searching specific types of data have been separated into ‘tabs’, arrayed at the top of the QuickSearch window. Several of the tabs contain entirely new search tools, such as a new ‘Simple’ search form, an easy–to–use tool with access to all the data types in FlyBase. More information on how to use QuickSearch can be found below.
 Links to specific help for each tab:
-[[FlyBase:QuickSearch#Simple tab| Simple tab]] |[[FlyBase:QuickSearch#Data Class tab| Data Class tab]] | [[FlyBase:QuickSearch#Expression tab| Expression tab]]  | [[FlyBase:QuickSearch#Gene Groups tab| Gene Groups tab]] | [[FlyBase:QuickSearch#GO tab| GO tab]]  | [[FlyBase:QuickSearch#Human Disease tab| Human Disease tab]]  | [[FlyBase:QuickSearch#Orthologs tab| Orthologs tab]] | [[FlyBase:QuickSearch#Phenotype tab| Phenotype tab]] | [[FlyBase:QuickSearch#Protein Domains tab| Protein Domains tab]] | [[FlyBase:QuickSearch#References tab| References tab]]
+[[FlyBase:QuickSearch#Simple tab| Simple tab]] | [[FlyBase:QuickSearch#Data Type tab| Data Type tab]]  |  [[FlyBase:QuickSearch#Expression tab| Expression tab]]  | [[FlyBase:QuickSearch#Phenotype tab| Phenotype tab]] |  [[FlyBase:QuickSearch#References tab| References tab]] | [[FlyBase:QuickSearch#GO tab| GO tab]]  |   [[FlyBase:QuickSearch#Protein Domain tab| Protein Domain tab]]  | [[FlyBase:QuickSearch#Gene Groups tab| Gene Groups tab]]  |  [[FlyBase:QuickSearch#Human Disease tab| Human Disease tab]]
 ===Species Searched===
-The Simple, Expression, and Data Class tabs search data that may be species-specific. In these tabs, a Species checkbox appears giving you the option to ‘include non-Dmel species’ in your search results. The default behavior is to return only Drosophila melanogaster (Dmel) data.
+Several tabs search data that may be species-specific. In these tabs, a Species checkbox appears giving you the option to ‘include non-Dmel species’ in your search results. The default behavior is to return only Drosophila melanogaster (Dmel) data.
-In the [[FlyBase:QuickSearch#Data Type tab| Data Class tab]], an override behavior is available. To search for data in a non-Dmel species you can add a 4-letter species prefix to the symbol you are using to search, separated by a backslash (‘\’). For example, if you type Dvir\dpp, the search results for the gene symbol dpp will be filtered for those associated with D. virilis only.
+In the [[FlyBase:QuickSearch#Data Type tab| Data Type tab]], an override behavior is available. To search for data in a non-Dmel species you can add a 4-letter species prefix to the symbol you are using to search, separated by a backslash (‘\’). For example, if you type Dvir\dpp, the search results for the gene symbol dpp will be filtered for those associated with D. virilis only.
 ===Controlled Vocabularies===
-Several QuickSearch tabs search FlyBase data by making use of controlled vocabulary (CV) terms. These tabs provide intuitive domain-specific searches of FlyBase reports based on the Gene Ontology (GO) controlled vocabulary, on anatomical, developmental-stage-specific or phenotypic class terms used to annotate phenotypes, and on anatomical and/or developmental-stage-specific terms used to annotate gene expression. Combinations of CV terms can be searched using the forms in these tabs. An auto-completion feature is active wherever a search term should come from a CV, to assist you in choosing terms that will match records in FlyBase. The various controlled vocabularies used in FlyBase can also be searched or browsed by clicking on the "Vocabularies" button above the QuickSearch box on the home page.
+Several QuickSearch tabs search FlyBase data by making use of controlled vocabulary (CV) terms. These tabs provide intuitive domain-specific searches of FlyBase reports based on the Gene Ontology (GO) controlled vocabulary, on anatomical, developmental-stage-specific or phenotypic class terms used to annotate phenotypes, and on anatomical and/or developmental-stage-specific terms used to annotate gene expression. Combinations of CV terms can be searched using the forms in these tabs. An auto-completion feature is active wherever a search term should come from a CV, to assist you in choosing terms that will match records in FlyBase.
 ===Auto-completion===
-The QuickSearch auto-completion feature is active in tabs that search FlyBase using [[FlyBase:QuickSearch#Controlled Vocabularies| controlled Vocabulary]] terms. Since only terms that are in the [[FlyBase:QuickSearch#Controlled Vocabularies| controlled Vocabulary]] will match records in FlyBase, the auto-completion feature suggests CV terms that are compatible with what you have typed. Selecting a term from the suggestion list reduces the possibility of a search returning nothing because the search term is not one that is used by FlyBase curators. The various controlled vocabularies used in FlyBase can also be searched or browsed by clicking on the "Vocabularies" button above the QuickSearch box on the home page.
+The QuickSearch auto-completion feature is active in tabs that search FlyBase using [[FlyBase:QuickSearch#Controlled Vocabularies| controlled Vocabulary]] terms. Since only terms that are in the [[FlyBase:QuickSearch#Controlled Vocabularies| controlled Vocabulary]] will match records in FlyBase, the auto-completion feature suggests CV terms that are compatible with what you have typed. Selecting a term from the suggestion list reduces the possibility of a search returning nothing because the search term is not one that is used by FlyBase curators.
-Some tabs for non-CV-based searches also use the auto-complete feature. Several of the searchable fields available in the [[FlyBase:QuickSearch#References tab| References tab]] are enhanced with auto-completion, which helps prevent searches that fail due to mis-spelled names or mis-remembered journal titles. Most of the data classes searchable under the [[FlyBase:QuickSearch#Data Type tab| Data Class tab]] have auto-completion associated with them as well.
+Some tabs for non-CV-based searches also use the auto-complete feature. Several of the searchable fields available in the [[FlyBase:QuickSearch#References tab| References tab]] are enhanced with auto-completion, which helps prevent searches that fail due to mis-spelled names or mis-remembered journal titles. Most of the data classes searchable under the [[FlyBase:QuickSearch#Data Type tab| Data Type tab]] have auto-completion associated with them as well.
-The QuickSearch auto-completion feature overrides your browser’s auto-completion function. '''Important Note''' -- In the Data Class and References tabs, the auto-complete function must be selected. If the auto-complete button is not checked, your browser's auto-complete function may operate and will offer options based on your history rather than valid FlyBase terms.
+The QuickSearch auto-completion feature overrides your browser’s auto-completion function.
-===Coordinated Auto-completion===
+'''Coordinated Auto-completion'''
 The coordinated auto-completion feature is active for tabs in which several search terms may be used simultaneously for a search. When a term has been entered in one of these fields, the coordinated auto-completion for the other fields is aware of the term already typed, and suggests only terms that actually occur in combination with the first term in FlyBase reports. Here is an example of how it works in the [[FlyBase:QuickSearch#Expression tab| Expression tab]]:
-In the '''Expression''' tab, text box fields for '''Stage, Tissue''', and '''Cell Loc.''' '''(cell location)''' are displayed. The auto-completion for these three fields is coordinated in the following sense: Suppose you enter "fertilized egg stage" in the '''Stage''' text box. When you move your focus to the Tissue text box, auto-complete there will show only four options; "egg", "female pronucleus", "fertilized egg", and "male pronucleus". This is because, out of the multitude of CV terms available for the '''Tissue''' field, only these four terms have actually been used in combination with "fertilized egg stage" by curators in an annotation captured in the FlyBase database. If you enter any other term in the '''Tissue''' text box, even though it may be a valid CV term for that field, your search would return zero hits, because there are no FlyBase reports containing that combination of CV terms.
+When the '''expression pattern (lit. curated)''' data class is selected, text box fields for '''Stage, Tissue''', and '''Cell Loc.''' '''(cell location)''' are displayed. The auto-completion for these three fields is coordinated in the following sense: Suppose you enter "fertilized egg stage" in the '''Stage''' text box. When you move your focus to the Tissue text box, auto-complete there will show only four options; "egg", "female pronucleus", "fertilized egg", and "male pronucleus". This is because, out of the multitude of CV terms available for the '''Tissue''' field, only these four terms have actually been used in combination with "fertilized egg stage" by curators in an annotation captured in the FlyBase database. If you enter any other term in the '''Tissue''' text box, even though it may be a valid CV term for that field, your search would return zero hits, because there are no FlyBase reports containing that combination of CV terms.
 Using the terms suggested by the auto-completion feature ensures that you do not enter terms that would be mutually exclusive (or are simply not used by curators) in FlyBase reports. Terms suggested by the auto-completion should always return results. If the coordinated auto-completion does not offer a term you wish to enter in a field, it is because this term does not appear in combination with some other term you have entered elsewhere on the form. In this case you should try another combination.
@@ Line 36: / Line 36: @@
 ===Wild Cards===
-When you use QuickSearch you can add the asterisk character ( * ) to the beginning or the end of a search term. This is recognized as a “wild card” and will find all terms that contain your search term at the end or beginning of a phrase, respectively. You can also flank your search term with wild card characters to find all phrases containing your search term. For example, you can find the genes that start with 'ft' by entering 'ft*'. (Search the Genes data class either under the [[FlyBase:QuickSearch#Simple tab| Simple tab]] by selecting the 'Genes' data class from the result summary table, or under the [[FlyBase:QuickSearch#Data Class tab| Data Class tab]] by selecting 'genes' from the '''Data Class''' drop-down menu.) The result of this search lists fat (ft) and fushi tarazu (ftz), as you would expect, and also fruitless (fru), because it has the synonym 'fty'.
+When you use QuickSearch you can add the asterisk character ( * ) to the beginning or the end of a search term. This is recognized as a “wild card” and will find all terms that contain your search term at the end or beginning of a phrase, respectively. You can also flank your search term with wild card characters to find all phrases containing your search term. For example, you can find the genes that start with 'ft' by entering 'ft*'. (Search the Genes data class either under the [[FlyBase:QuickSearch#Simple tab| Simple tab]] by selecting the 'Genes' data class from the result summary table, or under the [[FlyBase:QuickSearch#Data Type tab| Data Type tab]] by selecting 'genes' from the '''Data Class''' drop-down menu.) The result of this search lists fat (ft) and fushi tarazu (ftz), as you would expect, and also fruitless (fru), because it has the synonym 'fty'.
 ==Tab Descriptions==
@@ Line 48: / Line 48: @@
 ===Data Class tab===
-The Data Class tab allows searches that are restricted to only a single chosen data type.
+This tab contains a subset of the previous version of QuickSearch, and is laid out with very little change from that version. The Data Class drop-down menu restricts searches to only the single data type chosen, as before.
-Choose from among the 18 data types offered in the Data Class dropdown menu. There is also an "All data classes" option.
+The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active for most of the data classes in this tab.
-Choose to search just "ID/Symbol/Name" or search "All text" by clicking the appropriate box.
+===Expression tab===
+Search for genes according to expression patterns:
+At the top of this tab is a link to the [http://dev.flybase.org/static_pages/rna-seq/rna-seq_profile_search.html RNA-Seq Profile Search] tool. This tool can be used to search for genes by specifying a pattern of expression, as evidenced by high-throughput RNA-seq experiments.
+Use the form below this link to search curated statements that describe published accounts of transcript and polypeptide expression. The input form has input boxes for developmental '''Stage''', body part or '''Tissue''', and subcellular localization '''(Cell Loc.'''). The coordinated [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature will assist you in finding the appropriate [[FlyBase:QuickSearch#Controlled vocabularies| controlled vocabulary]] (CV) terms that have been used during the curation of each descriptor.
-Enter a symbol appropriate to the selected data type in the "Enter text" box.
+You can refine this search further by choosing to add '''qualifier terms'''. The coordinated [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature will provide you with a list of CV terms that have been used by curators to modify or limit the associated main term. The auto-completion for the qualifier terms is fully coordinated across all of these fields, in the sense that choosing a term for (e.g.) the Stage input will affect which qualifier terms are suggested for the Tissue or Cell Loc qualifier fields.
-Clicking the "QuickSearch autocomplete" option will enable the autocomplete function, which allows you to choose from among valid symbols for the selected data type. The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active for most of the data classes in this tab.
-If you'd like to include other species in your results, click on the "include non-Dmel" species box. The default behavior is to return only Drosophila melanogaster (Dmel) data. You can search for data in a particular non-melanogaster species by appending a 4-letter species prefix to the symbol you are using in your search, separated by a backslash (‘\’). For example, if you type Dvir\dpp, the search results for the gene symbol dpp will be filtered for those associated with D. virilis only.
+===Phenotype tab===
-'''Important Note''' -- The auto-complete function must be selected. If the auto-complete button is not checked, your browser's auto-complete function may operate and will offer options based on your history rather than valid FlyBase terms.
+Search for alleles that have particular phenotypes. The form is divided into two portions, which may be used independently or in combination. The coordinated [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature will assist you in finding the appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms that have been used during the curation of each phenotype.
-===Expression tab===
+The top section searches for alleles with a particular [http://{{SERVERNAME}}/cgi-bin/cvreport.html?id=FBcv:0000347 phenotypic class], e.g. "lethal" or "behavior defective". You can refine this search further using the refinement boxes, searching for a phenotype that occurs at a particular [http://{{SERVERNAME}}/cgi-bin/cvreport.html?id=FBdv:00007008 developmental stage], e.g. an embryonic stage and/or under particular conditions, e.g. "recessive" or "heat sensitive".
-Search for genes according to expression patterns:
+The bottom section searches for alleles that show a phenotype in a particular tissue or cell type, e.g. "wing" or "RP2 neuron". In this case, terms from the [http://{{SERVERNAME}}/cgi-bin/cvreport.html?id=FBbt:00000001Anatomy controlled vocabulary] or cellular component terms from the [http://geneontology.org/ Gene Ontology controlled vocabulary] are used. Again, you can refine this search further using the refinement boxes.
-The top part of the tab contains a form allowing searching of curated statements that describe published accounts of transcript and polypeptide expression as well expression associate with reporter constructs and insertions. The form has input boxes for developmental Stage, body part or Tissue, and subcellular localization (Cell Loc.). The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will assist you in finding an appropriate controlled vocabulary (CV) terms or combination of terms that have been used during the curation of each descriptor. Please note that if you fill one of the three boxes, the autocompleted options you will be offered in the other two boxes will include only terms that have been used with the term you have entered into the box or boxes you have already filled.
+Please note that the coordinated [[FlyBase:QuickSearch#Auto-completion| auto-completion]] works within the two sections, but not between them. This means it is possible even when using auto-completion suggestions, to search on a combination of terms entered in both sections of this form that will return zero hits.
-You can refine this search further by choosing to add qualifier terms. Click the "+" sign above the search boxes to bring up additional search boxes for entering qualifier terms. The [[FlyBase:QuickSearch#Coordinated Auto-completion| coordinated auto-completion]] feature will provide you with a list of CV terms that have been used by curators to modify or limit the associated main term. The auto-completion for the qualifier terms is fully coordinated across all of these fields, in the sense that choosing a term for (e.g.) the Stage input will affect which qualifier terms are suggested for the Tissue or Cell Loc qualifier fields.
+===References tab===
-Running the search will take you to a hit list of genes to which the search terms have been associated. To see other classes of hits (Alleles, Insertions, Recombinant Constructs), click on the associated green box at the top of the results page. To see the curated expression patterns, click on an item in the hit list and open the "Expression Data" section of the corresponding report.
+This tab searches the extensive FlyBase bibliography. Searches can be filtered by title/abstract text, journal name, publication type, and reference IDs (PubMed or FlyBase), in addition to the author and date filters. Appropriate fields also allow the use of Boolean operators, so you can search for papers authored by e.g. “Smith NOT Johnson”. In addition to Boolean operators the year field supports mathematical comparison symbols (>,>=,<,<=) and range indicators (-,--,..). For example,
-If you are looking for expression patterns of GAL4 drivers or lacZ reporters, choose the green box labeled "Alleles", click one of the blue arrows in the Symbol column to sort alphabetically, then scroll until you reach symbols that start with the text "Ecol\lacZ" (lacZ reporters) or "Scer\GAL4" (GAL4 drivers). Expression data is associated with the insertion or transgenic construct associated with the allele; the associated insertion or construct can be found on the allele report under the General Information section at the top of the report, under the fields "Associated Insertion(s)" and "Carried in Constructions". Alternatively, you can select all the alleles of interest in the Alleles hitlist, then select the Batch Download option from the HitList Conversion Tools button. In the Select Fields menu, choose "Associated insertion(s)" and "Carried in construct", found under the "Nature of the Allele" heading. This will generate a hitlist of the insertions and constructs to which the desired driver or reporter expression pattern have been curated.
-The bottom section of this tab contains a dropdown menu with links to a variety of RNA-Seq Search tools. GBrowse allows you to visually examine RNA-Seq expression levels in particular regions of the genome. The RNA-Seq Profile search can be used to search for genes that have a specific expression pattern of interest. RNA-Seq Similarity Search allows you to search for genes with a similar pattern of expression to the input gene. RNA-Seq by Region allows the comparison of RNA-Seq signals in a given region across samples or to compare signal between two regions in a single sample. Click on the link to the RNA-Seq overview page at the bottom of the tab to get a more detailed description of these RNA-Seq search options.
+>2003
+<=1945
+-2003
+-1990 NOT 1976
+OR 1995 OR 1998
+The QuickSearch auto-completion feature is active for the fields in this tab where it will be helpful, such as the journal name field. These fields are indicated with a superscript.
-===Gene Groups tab===
+===GO tab===
+Search the [[FlyBase:Gene Ontology (GO) Annotation| Gene Ontology]] (GO) [[FlyBase:Controlled Vocabularies| controlled vocabulary]] directly. Results are a CV term report, or list of reports. Once you are looking at the term report, you can then get a list of genes that are annotated with that GO term (look in the '''Records annotated with this exact term''' section), among other things. Please see the [[FlyBase:Vocabularies| CV term report help page]] for more information.
-Search the FlyBase-curated Gene Group data class using a gene or Gene Group symbol, name, synonym or ID.
+The QuickSearch  [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active in this tab.
-The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active in this tab.
+===Protein Domains tab===
-Click the 'browse' button to see a full list of Gene Groups.
+Search using InterPro IDs or signatures, including protein domains, families, repeats, and sites.
-===GO tab===
+Either start typing and select a term from the drop-down menu, or enter your own search term using wildcard(s) (*) if desired. Resulting hits will be genes whose protein products are annotated with an InterPro signature that wholly or partially matches your term. N.B. Search with an InterPro ID (e.g. 'IPR019956') if you wish to retrieve hits annotated with a specific InterPro signature.
-Search the [[FlyBase:Gene Ontology (GO) Annotation| Gene Ontology]] (GO) [[FlyBase:Controlled Vocabularies| controlled vocabulary]] directly. You can search all GO terms or limit your search to the molecular function, biological process, or cellular component GO vocabularies by selecting from the "Data Field" dropdown menu.
+See the InterPro [[http://www.ebi.ac.uk/interpro/faqs.html FAQ]] page for an explanation of these different signature types.
-Results are in the form of a hit list of matching GO terms. Clicking on the term of interest takes you to the term report from which, among other things, you can get a list of genes that are annotated with that GO term; look in the '''Records annotated with this exact term''' section. Please see the [[FlyBase:Vocabularies| Vocabularies]] help page for more information.
+The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active in this tab.
-The QuickSearch  [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active in this tab.
+===Gene Groups tab===
-===Human Disease tab===
+Search the FlyBase-curated Gene Group data class using a gene or Gene Group symbol, name, synonym or ID.
-Search the [http://disease-ontology.org/ Disease Ontology (DO)] by entering the name of a disease into the search box. The results are a hit list of matching Disease Ontology CV terms. Clicking on the disease of interest takes you to a term report from which, among other things, you can get a list of all genes or alleles that have been used to model, or interact with a model, of that disease in flies; you can also get to disease model reports which compile all of the disease model-related information on that disease in FlyBase. Please see the  [[FlyBase:Vocabularies| Vocabularies]] help page for more information.
+The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active in this tab.
-The QuickSearch auto-completion feature is active in this tab.
+Click the 'Browse' button to see a full list of Gene Groups.
-Click the 'browse' button to see a full list of Human Disease Model Reports.
+===Human Disease tab===
-===Orthologs tab===
+Search the [http://disease-ontology.org/ Disease Ontology (DO)] controlled vocabulary to find alleles that have been used as disease models. Enter the name of a disease into the search box. The results are a list of Disease Ontology CV reports that match the inputted term. From the CV report you can get a list of all genes or alleles that have been used to model, or interact with a model, of that disease in flies. Please see the  [[FlyBase:Vocabularies| CV term report help page]] for more information.
-This tab can be used to quickly search for orthologs of ''D. melanogaster'', human or other model organism genes, as provided by the [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl DRSC Integrative Ortholog Prediction Tool (DIOPT)] or [http://orthodb.org/ OrthoDB]. The DIOPT dataset integrates ortholog predictions for 8 model organisms from multiple tools and algorithms. (Further documentation is [http://www.flyrnai.org/DRSC-OPT.html here].) The OrthoDB dataset (as implemented in FlyBase) comprises ~40 species, biased towards those that are closely related to ''D. melanogaster'', and arranged into 5 ‘orthology groups’: Drosophila species, non-Drosophila Dipterans, non-Dipteran Insects, non-Insect Arthropods, non-Arthropod Metazoa.
+The QuickSearch auto-completion feature is active in this tab.
-To use, first select the input species by clicking on the '''Species''' dropdown menu. Next, enter one or more gene symbols/IDs in the adjacent '''Gene(s)''' box - multiple entries are accepted and need to be separated by spaces. (Response time will be proportional to the number of entries.) Then, select one or more output species using the '''check-boxes''' - where the input species is ''D. melanogaster'', there is a choice between searching the DIOPT or OrthoDB datasets. Finally, click the green '''Search''' button or press ‘enter’.
+===Orthology tab===
-The symbols/IDs that may be entered in the '''Gene(s)''' box depends on the 'input species', as follows:
+This tab can be used to quickly search for orthologs of ''D. melanogaster'', human or other model organism genes, as provided by the [http://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl DRSC Integrative Ortholog Prediction Tool (DIOPT)] or [http://orthodb.org/ OrthoDB]. The DIOPT dataset integrates ortholog predictions for 8 model organisms from multiple tools and algorithms. (Further documentation is [http://www.flyrnai.org/DRSC-OPT.html here].) The OrthoDB dataset (as implemented in FlyBase) comprises ~40 species, biased towards those that are closely related to ''D. melanogaster'', and arranged into 5 ‘orthology groups’.
-{| class="wikitable"
-|-
-! Input species !! Allowable symbols/IDs (example)
-|-
-| ''H. sapiens'' || [http://www.genenames.org/ HGNC] gene symbol (e.g. CDK1) or gene ID (e.g. HGNC:1722); [http://omim.org OMIM] ID (e.g. OMIM_GENE:116940); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. '983); [http://www.ensembl.org/ Ensembl] ID (e.g. ENSG00000170312)
-|-
-| ''M. musculus'' || [http://www.informatics.jax.org MGI] gene symbol (e.g. Cdk1) or gene ID (e.g. MGI:88351); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 12534)
-|-
-| ''X. tropicalis'' || [http://www.xenbase.org XenBase] gene symbol (e.g. cdk1) or gene ID (e.g. XB-GENE-482750); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 394503)
-|-
-| ''D. rerio'' || [http://zfin.org/ ZFIN] gene symbol (e.g. cdk1) or gene ID (e.g. ZDB-GENE-010320-1); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 80973)
-|-
-| ''D. melanogaster'' || [http://www.flybase.org FlyBase] gene symbol (e.g. Cdk1), annotation symbol (e.g. CG5363), or gene ID (e.g. FBgn0004106); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 34411)
-|-
-| ''C. elegans'' || [http://www.wormbase.org WormBase] gene symbol (e.g. cdk-1) or gene ID (e.g. WBGene00000405); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 176374)
-|-
-| ''S. cerevisiae'' || [http://www.yeastgenome.org SGD] gene symbol (e.g. CDC28) or gene ID (e.g. S000000364); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 852457)
-|-
-| ''S. pombe'' || [http://www.pombase.org PomBase] gene symbol (e.g. cdc2); [http://www.ncbi.nlm.nih.gov/gene NCBI Gene] ID (e.g. 2539869)
-|-
-|}
-Note that symbol-based searches are case-sensitive - to ensure validity, users should select a gene symbol from the auto-suggest list that appears when typing. (Auto-suggest works only for the first entered symbol.) Also note that this tool does not support searching using gene fullnames.
+To use, first select the input species by clicking on the '''Species''' drop-down menu. Next, enter one or more gene symbols/IDs in the adjacent '''Gene(s)''' box - multiple entries need to be separated by spaces. Then, select one or more output species using the '''check-boxes''' - where the input species is ''D. melanogaster'', there is a choice between searching the DIOPT or OrthoDB datasets. Finally, click the green '''Search''' button or press ‘enter’.
+If the input species is ''D. melanogaster'', then FlyBase gene symbols (e.g. ‘park’), annotation symbols (e.g. ‘CG10523’) or gene IDs (e.g. ‘FBgn0041100’) can be entered in the '''Gene(s)''' box. For other species, model organism database symbols (e.g. ’PARK2’) or IDs (e.g. ‘HGNC:8607’), or NCBI Gene IDs (e.g. ‘5071’) or Ensembl IDs (e.g. ‘ENSG00000185345’) can be entered. Note that symbol-based searches are case-sensitive - to ensure validity, users should select a gene symbol from the auto-suggest list that appears while typing. This tool does not support searching using gene fullnames.
-On the results page, the top row shows the search term, species, the matched gene symbol, and any relevant links to Gene Reports. Below this are the column headers, followed by the list of ortholog predictions arranged by species.
+On the results page, the top row shows the search term, species, the matched gene symbol, and any relevant links. Below this are the column headers, followed by the list of ortholog predictions arranged by species.
 For DIOPT-based searches, the columns are:
-* '''Ortholog Gene''': official gene symbol, as used in the relevant model organism database
+* '''Ortholog Gene''': official gene symbol, as used in model organism database
 * '''Ortholog Gene Reports''': links to report pages at model organism databases, NCBI, Ensembl and/or OMIM
 * '''Score''': a simple score indicating the number of tools that support a given orthologous gene-pair relationship
-* '''Best Score''': either ‘yes’ or ‘no’, indicating whether the given ortholog has the highest score for the query gene within that species
+* '''Best Score''': either ‘yes’ or ‘no’ to indicate whether the given ortholog has the highest score for the query gene
-* '''Best Rev Score''': either ‘yes’ or ‘no’, indicating whether the query gene has the highest score for the given ortholog in the reciprocal search; also includes a link to show the full results of performing the reciprocal search (among those species selected in the original query)
+* '''Best Rev Score''': either ‘yes’ or ‘no’ to indicate whether the query gene has the highest score for the given ortholog in the reciprocal search
+* '''Align''': link to an alignment between the given orthologous gene-pairs on the DIOPT site
 * '''Source''': list of individual ortholog prediction tools that support a given orthologous gene-pair relationship
-* '''Align''': link to an alignment between the given orthologous gene-pairs on the DIOPT site
 * '''Transgene in Fly''': link to a FlyBase Gene Report for a non-Drosophila gene, indicating that that gene has been expressed transgenically in Drosophila
-The results page for OrthoDB-based searches is similar, except that the DIOPT-specific columns are absent and the ‘Source’ column lists only ‘OrthoDB’. The 'orthology group' to which the species belongs is shown on the right side of each species line.
+The results page is similar for OrthoDB-based searches, except that the DIOPT-specific columns are removed and the ‘Source’ column lists only ‘OrthoDB’.
 In cases where there are multiple hits to a single search term (as may happen when a numerical ID is entered), then all hits together with their predicted orthologs are shown in the results table.
-Clicking on the '''Save results as tsv file''' text at the top of the results page will download all the results shown in that page to a file in tab separated value format, with one orthologous gene-pair per line. It has the following columns:
-* query_context: the entered search term
-* query_species: the selected input species
-* query_gene: the matched input gene symbol
-* target_species: the selected output species
-* ortholog_gene: official gene symbol, as used in the relevant model organism database
-* ortholog_gene_reports: gene IDs at model organism databases, NCBI, Ensembl and/or OMIM
-* source: list of individual ortholog prediction tools that support a given orthologous gene-pair relationship
-* score: a simple score indicating the number of tools that support a given orthologous gene-pair relationship
-* best_score: either ‘yes’ or ‘no’ to indicate whether the given ortholog has the highest score for the query gene
-* best_reverse_score: either ‘yes’ or ‘no’ to indicate whether the query gene has the highest score for the given ortholog in the reciprocal search
-* transgene_in_fly: Where applicable, the FlyBase gene ID and symbol for a non-Drosophila gene where that gene has been expressed transgenically in Drosophila
-The columns for OrthoDB-based searches are similar, except that the DIOPT-specific columns are absent and the ‘Source’ column lists only ‘OrthoDB’.
-===Phenotype tab===
-Search for alleles that have particular phenotypes. The form is divided into two portions, which may be used independently or in combination. The coordinated [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature will assist you in finding the appropriate [[FlyBase:QuickSearch#Controlled Vocabularies| controlled vocabulary]] (CV) terms that have been used during the curation of each phenotype.
-The top section searches for alleles with a particular [http://{{SERVERNAME}}/cgi-bin/cvreport.html?id=FBcv:0000347 phenotypic class], e.g. "lethal" or "behavior defective". You can refine this search further using the refinement boxes, searching for a phenotype that occurs at a particular [http://{{SERVERNAME}}/cgi-bin/cvreport.html?id=FBdv:00007008 developmental stage], e.g. an embryonic stage and/or under particular conditions, e.g. "recessive" or "heat sensitive".
-The bottom section searches for alleles that show a phenotype in a particular tissue or cell type, e.g. "wing" or "RP2 neuron". In this case, terms from the [http://{{SERVERNAME}}/cgi-bin/cvreport.html?id=FBbt:00000001Anatomy controlled vocabulary] or cellular component terms from the [http://geneontology.org/ Gene Ontology controlled vocabulary] are used. Again, you can refine this search further using the refinement boxes.
-Please note that the coordinated [[FlyBase:QuickSearch#Auto-completion| auto-completion]] works within the two sections, but not between them. This means it is possible even when using auto-completion suggestions, to search on a combination of terms entered in both sections of this form that will return zero hits.
-===Protein Domains tab===
-Search using InterPro IDs or signatures, including protein domains, families, repeats, and sites.
-Either start typing and select a term from the drop-down menu, or enter your own search term using wildcard(s) (*) if desired. Resulting hits will be genes whose protein products are annotated with an InterPro signature that wholly or partially matches your term. N.B. Search with an InterPro ID (e.g. 'IPR019956') if you wish to retrieve hits annotated with a specific InterPro signature.
-See the InterPro [[http://www.ebi.ac.uk/interpro/faqs.html FAQ]] page for an explanation of these different signature types.
-The QuickSearch [[FlyBase:QuickSearch#Auto-completion| auto-completion]] feature is active in this tab.
-===References tab===
-This tab searches the extensive FlyBase bibliography. Searches can be filtered by title/abstract text, journal name, publication type, and reference IDs (PubMed or FlyBase), in addition to the author and date filters. Appropriate fields also allow the use of Boolean operators, so you can search for papers authored by e.g. “Smith NOT Johnson”. In addition to Boolean operators, the year field supports mathematical comparison symbols (>,>=,<,<=) and range indicators (-,--,..). For example,
->2003
-<=1945
--2003
--1990 NOT 1976
-OR 1995 OR 1998
-The QuickSearch auto-completion feature is active for the fields in this tab where it will be helpful, such as the journal name field. These fields are indicated with a superscript.
-'''Important Note''' -- The auto-complete function must be selected. If the auto-complete button is not checked, your browser's auto-complete function may operate and will offer options based on your history rather than valid FlyBase terms.