Difference between revisions of "FlyBase:Vocabularies Tool"
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| − | + | =Brief Description= | |
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| − | The Vocabularies tool allows you to search the controlled vocabularies (CVs) used by FlyBase and takes you to the associated | + | The Vocabularies tool allows you to search the '''[[FlyBase:Controlled vocabularies used by FlyBase | controlled vocabularies (CVs)]]''' used by FlyBase and takes you to the associated CV term reports. Term reports display a definition, synonyms, and references, show how a particular term relates to other terms within the same controlled vocabulary hierarchy, and provide links to objects in FlyBase that have been annotated with the term. For a field-by-field description of the CV Term reports see [[FlyBase:Vocabularies | '''CV Term Report Help''']]. |
| − | + | =Video Tutorials= | |
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| − | See the related video tutorials | + | See the related video tutorials |
| − | + | ::[https://www.youtube.com/watch?v=jgCON15SiRo Finding related genes/alleles in FlyBase: Vocabularies] | |
| − | + | ::[https://www.youtube.com/watch?v=XFCR8BRfGp0 Finding related genes in FlyBase: The Gene Ontology] | |
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| + | =How to Search using Vocabularies= | ||
First choose the particular CV heirarchy you would like to search such as "FlyBase anatomy (FBbt)" or "Gene Ontology (GO)" from the "CV Heirarchy pull-down menu. Alternatively, use the default option, which is to search all of the FlyBase CVs. | First choose the particular CV heirarchy you would like to search such as "FlyBase anatomy (FBbt)" or "Gene Ontology (GO)" from the "CV Heirarchy pull-down menu. Alternatively, use the default option, which is to search all of the FlyBase CVs. | ||
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Click on the CV term to go to the term report page for that term. | Click on the CV term to go to the term report page for that term. | ||
| − | + | =Search Examples= | |
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| − | + | =Search Hints= | |
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| − | Wild cards (*) can be added to the beginning or the end of a search term. For example, searching for the term ‘pup*’ finds any term whose name or synonyms contain a word that starts with 'pup' (e.g. pupa, pupal dorsal branch, protein pupylation, pharate adult stage P11, which has the synonym pupal stage P11), while searching with ‘*pup*’ finds any term with 'pup' anywhere within any of the words of the name or synonyms (e.g. prepupa, and prepupal epidermis). | + | '''Wild cards''' (*) can be added to the beginning or the end of a search term. For example, searching for the term ‘pup*’ finds any term whose name or synonyms contain a word that starts with 'pup' (e.g. pupa, pupal dorsal branch, protein pupylation, pharate adult stage P11, which has the synonym pupal stage P11), while searching with ‘*pup*’ finds any term with 'pup' anywhere within any of the words of the name or synonyms (e.g. prepupa, and prepupal epidermis). |
| − | + | =Browsing the CV heirarchies= | |
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| − | Instead of a doing a direct search, you may choose to browse different CV hierarchies using the interface below the horizontal line. Select the radio-button for the Vocabulary type of choice on the left and then click on a term in the top level CV hierarchy tree in the grey box on the right. This will take you to a term report from which you can explore the tree (See hints on exploring the CV hierarchy In the [[FlyBase:Vocabularies | CV Term Report | + | Instead of a doing a direct search, you may choose to browse different CV hierarchies using the interface below the horizontal line. Select the radio-button for the Vocabulary type of choice on the left and then click on a term in the top level CV hierarchy tree in the grey box on the right. This will take you to a term report from which you can explore the tree (See hints on exploring the CV hierarchy In the [[FlyBase:Vocabularies | CV Term Report]] Help page). |
| − | + | =Types of information accessible from CV Term Reports= | |
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| − | Each term report allows you to retrieve any gene, allele, insertion, construct, Human disease, or image reports annotated with this term or with any of its children, using the buttons in the section ”'Records annotated with this term OR any of its CHILD TERMS”. | + | *Each term report allows you to retrieve any gene, allele, insertion, construct, Human disease, or image reports annotated with this term or with any of its children, using the buttons in the section ”'Records annotated with this term OR any of its CHILD TERMS”. |
Some of the types of information that you can access from term reports is listed below: | Some of the types of information that you can access from term reports is listed below: | ||
| − | To find out how many genes have been curated with a particular GO term within FlyBase, search Vocabularies for the appropriate GO term and click on the 'Genes' box. | + | *To find out how many genes have been curated with a particular GO term within FlyBase, search Vocabularies for the appropriate GO term and click on the 'Genes' box. |
| − | To find genes or constructs that are expressed within a particular part of the fly's anatomy, search with the desired anatomy term and click on the 'Genes' or 'Insertions' boxes. The same strategy can be used to find which genes are expressed at a certain stage of development. | + | *To find genes or constructs that are expressed within a particular part of the fly's anatomy, search with the desired anatomy term and click on the 'Genes' or 'Insertions' boxes. The same strategy can be used to find which genes are expressed at a certain stage of development. |
| − | If you are interested in a particular phenotype and want to search for all alleles that have been known to cause it, search for the phenotypic class term and click on the 'Alleles' box. | + | *If you are interested in a particular phenotype and want to search for all alleles that have been known to cause it, search for the phenotypic class term and click on the 'Alleles' box. |
| − | To find alleles that are a model of a human disease, ameliorate and exacerbate it, search for the disease name. Clicking on the top 'Alleles' box will return alleles in either of those categories. To search for alleles that are within a specific category, e.g. are a model of a human disease, use the 'Compound Statements' section. | + | *To find alleles that are a model of a human disease, ameliorate and exacerbate it, search for the disease name. Clicking on the top 'Alleles' box will return alleles in either of those categories. To search for alleles that are within a specific category, e.g. are a model of a human disease, use the 'Compound Statements' section. |
Latest revision as of 23:51, 23 January 2018
Brief Description
The Vocabularies tool allows you to search the controlled vocabularies (CVs) used by FlyBase and takes you to the associated CV term reports. Term reports display a definition, synonyms, and references, show how a particular term relates to other terms within the same controlled vocabulary hierarchy, and provide links to objects in FlyBase that have been annotated with the term. For a field-by-field description of the CV Term reports see CV Term Report Help.
Video Tutorials
See the related video tutorials
How to Search using Vocabularies
First choose the particular CV heirarchy you would like to search such as "FlyBase anatomy (FBbt)" or "Gene Ontology (GO)" from the "CV Heirarchy pull-down menu. Alternatively, use the default option, which is to search all of the FlyBase CVs.
Then search for a specific CV term by entering the official CV term name, the term identification number, or a synonym for the term in the "Enter text" box and clicking on "Search". The autocomplete feature, guided by the text that you type, provides help with finding valid CV terms. For each search performed, the Vocabularies tool returns a hit list of CV term reports that match the search term. These are listed alphabetically in the following order: terms whose name starts with the search query, terms whose name contains the search query, terms whose synonyms contain the search query. Obsoleted terms (no longer used for annotation) are shown at the bottom.
Click on the CV term to go to the term report page for that term.
Search Examples
| Example Search Term | Controlled vocabulary | Notes |
|---|---|---|
| Malpighian tubule | Anatomy | This is the official CV name |
| mushroom body heel | Anatomy | This is a synonym for mushroom body spur |
| GO:0005703 | GO: Cellular Component | This is the ID for polytene chromosome puff |
| tracheal liquid clearance | GO: Biological Process | This is the official CV term |
| third instar larval stage | Development | This is the official CV term |
| EMS | Other FlyBase CV | This is a synonym for ethyl methanesulfonate |
Search Hints
Wild cards (*) can be added to the beginning or the end of a search term. For example, searching for the term ‘pup*’ finds any term whose name or synonyms contain a word that starts with 'pup' (e.g. pupa, pupal dorsal branch, protein pupylation, pharate adult stage P11, which has the synonym pupal stage P11), while searching with ‘*pup*’ finds any term with 'pup' anywhere within any of the words of the name or synonyms (e.g. prepupa, and prepupal epidermis).
Browsing the CV heirarchies
Instead of a doing a direct search, you may choose to browse different CV hierarchies using the interface below the horizontal line. Select the radio-button for the Vocabulary type of choice on the left and then click on a term in the top level CV hierarchy tree in the grey box on the right. This will take you to a term report from which you can explore the tree (See hints on exploring the CV hierarchy In the CV Term Report Help page).
Types of information accessible from CV Term Reports
- Each term report allows you to retrieve any gene, allele, insertion, construct, Human disease, or image reports annotated with this term or with any of its children, using the buttons in the section ”'Records annotated with this term OR any of its CHILD TERMS”.
Some of the types of information that you can access from term reports is listed below:
- To find out how many genes have been curated with a particular GO term within FlyBase, search Vocabularies for the appropriate GO term and click on the 'Genes' box.
- To find genes or constructs that are expressed within a particular part of the fly's anatomy, search with the desired anatomy term and click on the 'Genes' or 'Insertions' boxes. The same strategy can be used to find which genes are expressed at a certain stage of development.
- If you are interested in a particular phenotype and want to search for all alleles that have been known to cause it, search for the phenotypic class term and click on the 'Alleles' box.
- To find alleles that are a model of a human disease, ameliorate and exacerbate it, search for the disease name. Clicking on the top 'Alleles' box will return alleles in either of those categories. To search for alleles that are within a specific category, e.g. are a model of a human disease, use the 'Compound Statements' section.