Toward Single Neuron Gene Expression Analysis for Studying Behavior
Toward a Unified Gene Page
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Transcript of Toward a Unified Gene Page
![Page 2: Toward a Unified Gene Page](https://reader036.fdocuments.in/reader036/viewer/2022062321/56812aa6550346895d8e67ed/html5/thumbnails/2.jpg)
• Bionet news (www.bio.net) needs new home• Used by celegans, yeast, chlamydomonas,
drosophila, zebrafish, maize, urodeles; genbank, embl, software, others. Letters of Support?
• TeraGrid (NSF Shared Cyberinfrastructure) wants to help MOD genome computes • BLAST for FlyBase and euGenes this fall - others?
- See Don Gilbert for details
Extraneous announcements
![Page 3: Toward a Unified Gene Page](https://reader036.fdocuments.in/reader036/viewer/2022062321/56812aa6550346895d8e67ed/html5/thumbnails/3.jpg)
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• Common parts of MOD gene pages• What could/should be unified?• Who will benefit? Costs?
• Common Web Reports and XML ?• You: discuss, design common gene page
Gene Pages
![Page 5: Toward a Unified Gene Page](https://reader036.fdocuments.in/reader036/viewer/2022062321/56812aa6550346895d8e67ed/html5/thumbnails/5.jpg)
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• Names, symbols/IDs, synonyms• Map locations• Sequences• Reagents• Gene ontology• Similar Genes• Database cross-refs, External links
Common gene attributes, pt1
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• Alleles, Transcripts• Expression and Mutant Phenotypes• Proteins, Structure and Domains• Gene Interactions• Literature references• Summary Text• ... others...
Common gene attributes, pt2
![Page 8: Toward a Unified Gene Page](https://reader036.fdocuments.in/reader036/viewer/2022062321/56812aa6550346895d8e67ed/html5/thumbnails/8.jpg)
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• Labels - are these same things?• Gene / locus / orf
• Homolog / ortholog / relationship / similarity
• Citation / publication / reference
• Organization of document
• Section headers
• Important at top, common ordering
Should these be unified?
![Page 10: Toward a Unified Gene Page](https://reader036.fdocuments.in/reader036/viewer/2022062321/56812aa6550346895d8e67ed/html5/thumbnails/10.jpg)
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• Structure and size of default document
• Tabular, text, document-like, …
• One screen or long report
• Graphics (maps, icons, ...)
• Further Detail options
• Layout and Design (colors, formatting, fonts ..)
Should these be unified?
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• MOD customizations• Look and Feel
• Details & Extensions
• Customer choices• Best for organism community (org. standard)
or for general reader (general standard)• Best for beginners or experts
(simple,complex)
What is customizable?
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• Computable text of gene page ?• "what you see (web page) is also what your
computer can read"• simple and human-readable, or complex and
detailed
• XML variants, tabular, other?• Ace2XML, NCBI XML, others
• Samples (Web -> XML)
Common Gene XML?
![Page 20: Toward a Unified Gene Page](https://reader036.fdocuments.in/reader036/viewer/2022062321/56812aa6550346895d8e67ed/html5/thumbnails/20.jpg)
Fly Gene Page as XML
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Yeast Gene Page as XML
![Page 22: Toward a Unified Gene Page](https://reader036.fdocuments.in/reader036/viewer/2022062321/56812aa6550346895d8e67ed/html5/thumbnails/22.jpg)
Mouse Gene Page as XML
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Worm Gene Page as XML
![Page 24: Toward a Unified Gene Page](https://reader036.fdocuments.in/reader036/viewer/2022062321/56812aa6550346895d8e67ed/html5/thumbnails/24.jpg)
• Now: Design your common gene page• Cut/paste sample XML pages into one
• Comment on what should be unified
• Comment on best parts of MOD pages
• After: Talk MODs into generating these
http://eugenes.org/all/gene-report-examples/
HTML and XML
Tasks