FlyBase Reference Manual Table of Contents

RefMan Sections RefMan Table of Contents FlyBase Documents

FlyBase Reference Manual

Reference Manual A. Getting Started With FlyBase
- A.1. What Is FlyBase?
- A.2. How to Access FlyBase
- A.3. How to Use FlyBase
- A.4. How to Contact FlyBase
- A.5. Learning More About FlyBase
Reference Manual B. Detailed Descriptions of FlyBase Structure and Data
- B.1. Genes
  - B.1.1. General description of Genes data
  - B.1.2. List of Genes field descriptions
  - B.1.3. Detailed description of the Genes fields
  - B.1.4. Nontraditional alleles
  - B.1.4.1. Alleles of reporter genes
  - B.1.4.2. Alleles of ectopically expressed Drosophila gene products
  - B.1.4.3. Alleles of ectopically expressed non-Drosophila effector products
  - B.1.4.4. Classical alleles engineered into transposons, including rescue constructs
  - B.1.5. Protein and transcript symbols and exon naming
  - B.1.6. FlyBase Genes - Interactive Fly Cross Index
  - B.1.7. Differences and omissions from Lindsley and Zimm (1992)
- B.2. Synonyms
- B.3. Species other than D. melanogaster
- B.4. Genetic objects from non-Drosophila species that are included in Drosophila
- B.5. Maps
  - B.5.1. Sequence-based Maps
  - B.5.1.1. Genome Browser, Gbrowse
  - B.5.1.2. Drosophila Genome Overview
  - B.5.1.3. Apollo
  - B.5.2. Gene Order Maps
  - B.5.3. Computed Aberration Breakpoints and Cytological Locations of Genes
- B.6. Wild genotypes and Chromosomes
- B.7. Function and Structure of Gene Products
- B.8. Aberrations
  - B.9.1. List of Aberrations field descriptions
  - B.9.2. Detailed description of the Aberrations fields
- B.9. Transposons and transposon insertions
- B.10. Stocks
- B.11. Genomic Clones and STSs
  - B.11.1. Cosmids and cosmid STSs
  - B.11.2. P1 clones and P1 STSs
  - B.11.3. BAC clones and BAC STSs
  - B.11.4. Drosophila virilis P1 clones
  - B.11.5. YACs
- B.12. References - the Drosophila Bibliography
  - B.12.1. Reference formats
  - B.12.2. Reference classes
  - B.12.3. Journals and multi-author works
  - B.12.4. Reference sources
  - B.12.5. Copyright statements
- B.13. People
- B.14. Anatomy and Images
Reference Manual C. Using FlyBase on the Web
- C.1. Reaching the FlyBase Homepage
- C.2. Report Options - Viewing FlyBase Data
- C.3. FlyBase Search Tools
  - C.3.1. Quick Search
  - C.3.2. Advanced Searchs
    - C.3.2.1. Examples of Genes Queries
    - C.3.2.2. Searching Stock Lists
    - C.3.2.3. Searching for Transgene Constructs and Insertions
    - C.3.2.4. Searching References
    - C.3.2.5. Greek symbols in Queries
    - C.3.2.6. Other Database Accession Identifiers in Queries
  - C.3.3. Multipurpose Search Tools
    - C.3.3.1. Batch Download by ID
    - C.3.3.2. CytoSearch
    - C.3.3.3. Gene Expression Summaries
    - C.3.3.4. Anatomy Image Browser
- C.4. Data Selection-Impact on Query Results
Reference Manual D. Bulk FlyBase Data Retrieval
- D.1. Bulk FlyBase data by Web query
  - D.1.1. Bulk reports from a search page
  - D.1.2. Batch download by ID
  - D.1.3. Bulk retrieval for any query
- D.2. Bulk FlyBase data by FTP
  - D.2.1. The file structure of FlyBase
  - D.2.2. Bulk data in ACODE and XML formats
  - D.2.3. Retrieving file
Reference Manual E. Portable FlyBase Server
Reference Manual F. Links to and from FlyBase
- F.1. FlyBase Identifier Numbers
- F.2. Other links to FlyBase
- F.3. Links to Drosophila data outside of FlyBase
  - F.3.1. FlyBase-curated links
  - F.3.2. FlyBase linkouts
- F.4. Links to non-Drosophila orthologs
Reference Manual G. FlyBase Documentation
- G.1. Genetic nomenclature of Drosophila
- G.2. Controlled vocabularies used by FlyBase
- G.3. FlyBase working papers
- G.4. The Redbook
- G.5. Greybook Errors - Ashburner (1989)
- G.6. Personal communications to FlyBase
- G.7. Announcements and News
Reference Manual H. Allied Data
Reference Manual I. The FlyBase Project
- I.1. The copyright of FlyBase
- I.2. How to reference FlyBase
- I.3. How to contact FlyBase
- I.4. The FlyBase Consortium
- I.5. The FlyBase Advisors
- I.6. Acknowledgments