Difference between revisions of "Annotation Dependencies"
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| + | ==Annotation data required by certain components== | ||
| + | geWorkbench currently can only read in annotation files based on the Affymetrix annotation file format. Following is a list of the column headers for data types required by various geWorkbench components. | ||
| + | |||
| + | * All components require "'''Probe Set ID'''". | ||
{| border="1" cellpadding="5" cellspacing="0" style="margin:10px;" | {| border="1" cellpadding="5" cellspacing="0" style="margin:10px;" | ||
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!Columns required | !Columns required | ||
| + | |- | ||
|CNKB | |CNKB | ||
| − | | | + | |Entrez Gene |
| + | |- | ||
|Gene Ontology | |Gene Ontology | ||
| − | | | + | |Gene Ontology Biological Process, Gene Ontology Cellular Component, Gene Ontology Molecular Function |
| + | |- | ||
|Marker Annotations | |Marker Annotations | ||
| | | | ||
| + | |- | ||
|Sequence Retrieval (EBI) | |Sequence Retrieval (EBI) | ||
| | | | ||
| + | |- | ||
|Sequence Retrieval (Santa Cruz) | |Sequence Retrieval (Santa Cruz) | ||
| | | | ||
|} | |} | ||
| + | |||
| + | |||
| + | ==List of All Affy headers== | ||
| + | |||
| + | * Probe Set ID | ||
| + | * GeneChip Array | ||
| + | * Species Scientific Name | ||
| + | * Annotation Date | ||
| + | * Sequence Type | ||
| + | * Sequence Source | ||
| + | * Transcript ID(Array Design) | ||
| + | * Target Description | ||
| + | * Representative Public ID | ||
| + | * Archival UniGene Cluster | ||
| + | * UniGene ID | ||
| + | * Genome Version | ||
| + | * Alignments | ||
| + | * Gene Title | ||
| + | * Gene Symbol | ||
| + | * Chromosomal Location | ||
| + | * Unigene Cluster Type | ||
| + | * Ensembl | ||
| + | * Entrez Gene | ||
| + | * SwissProt | ||
| + | * EC | ||
| + | * OMIM | ||
| + | * RefSeq Protein ID | ||
| + | * RefSeq Transcript ID | ||
| + | * FlyBase | ||
| + | * AGI | ||
| + | * WormBase | ||
| + | * MGI Name | ||
| + | * RGD Name | ||
| + | * SGD accession number | ||
| + | * Gene Ontology Biological Process | ||
| + | * Gene Ontology Cellular Component | ||
| + | * Gene Ontology Molecular Function | ||
| + | * Pathway | ||
| + | * InterPro | ||
| + | * Trans Membrane | ||
| + | * QTL | ||
| + | * Annotation Description | ||
| + | * Annotation Transcript Cluster | ||
| + | * Transcript Assignments | ||
| + | * Annotation Notes | ||
Latest revision as of 16:04, 18 June 2010
Annotation data required by certain components
geWorkbench currently can only read in annotation files based on the Affymetrix annotation file format. Following is a list of the column headers for data types required by various geWorkbench components.
- All components require "Probe Set ID".
| Component | Columns required |
|---|---|
| CNKB | Entrez Gene |
| Gene Ontology | Gene Ontology Biological Process, Gene Ontology Cellular Component, Gene Ontology Molecular Function |
| Marker Annotations | |
| Sequence Retrieval (EBI) | |
| Sequence Retrieval (Santa Cruz) |
List of All Affy headers
- Probe Set ID
- GeneChip Array
- Species Scientific Name
- Annotation Date
- Sequence Type
- Sequence Source
- Transcript ID(Array Design)
- Target Description
- Representative Public ID
- Archival UniGene Cluster
- UniGene ID
- Genome Version
- Alignments
- Gene Title
- Gene Symbol
- Chromosomal Location
- Unigene Cluster Type
- Ensembl
- Entrez Gene
- SwissProt
- EC
- OMIM
- RefSeq Protein ID
- RefSeq Transcript ID
- FlyBase
- AGI
- WormBase
- MGI Name
- RGD Name
- SGD accession number
- Gene Ontology Biological Process
- Gene Ontology Cellular Component
- Gene Ontology Molecular Function
- Pathway
- InterPro
- Trans Membrane
- QTL
- Annotation Description
- Annotation Transcript Cluster
- Transcript Assignments
- Annotation Notes
