ubic.gemma.core.analysis.service

Interface ArrayDesignAnnotationService

All Known Implementing Classes:

ArrayDesignAnnotationServiceImpl

public interface ArrayDesignAnnotationService

Methods to generate annotations for array designs, based on information already in the database. This can be used to generate annotation files used for ermineJ, for example. The file format:

• The file is tab-delimited text. Comma-delimited files or Excel spreadsheets (for example) are not supported.
• There is a one-line header included in the file for readability.
• The first column contains the probe identifier
• The second column contains a gene symbol(s). Clusters are delimited by '|' and genes within clusters are delimited by ','
• The third column contains the gene names (or description). Clusters are delimited by '|' and names within clusters are delimited by '$'
• The fourth column contains a delimited list of GO identifiers. These include the "GO:" prefix. Thus they read "GO:00494494" and not "494494". Delimited by '|'.

Note that for backwards compatibility, GO terms are not segregated by gene cluster.

Author:

paul

Nested Class Summary

Nested Classes

Modifier and Type	Interface and Description
static class	ArrayDesignAnnotationService.OutputType

Field Summary

Fields

Modifier and Type	Field and Description
static String	ANNOT_DATA_DIR
static String	ANNOTATION_FILE_SUFFIX
static String	BIO_PROCESS_FILE_SUFFIX
static String	NO_PARENTS_FILE_SUFFIX
static String	STANDARD_FILE_SUFFIX String included in file names for standard (default) annotation files.

Method Summary

Modifier and Type	Method and Description
void	create(ArrayDesign inputAd, Boolean overWrite) Create (or update) all the annotation files for the given platform.
void	deleteExistingFiles(ArrayDesign arrayDesign)
int	generateAnnotationFile(Writer writer, Collection<Gene> genes) Generate an annotation for a list of genes, instead of probes.

Field Detail

ANNOTATION_FILE_SUFFIX

static final String ANNOTATION_FILE_SUFFIX

See Also:

Constant Field Values

BIO_PROCESS_FILE_SUFFIX

static final String BIO_PROCESS_FILE_SUFFIX

See Also:

Constant Field Values

NO_PARENTS_FILE_SUFFIX

static final String NO_PARENTS_FILE_SUFFIX

See Also:

Constant Field Values

STANDARD_FILE_SUFFIX

static final String STANDARD_FILE_SUFFIX

String included in file names for standard (default) annotation files. These include GO terms and all parents.

See Also:

Constant Field Values

ANNOT_DATA_DIR

static final String ANNOT_DATA_DIR

Method Detail

deleteExistingFiles

void deleteExistingFiles(ArrayDesign arrayDesign)

create

void create(ArrayDesign inputAd,
            Boolean overWrite)
     throws IOException

Create (or update) all the annotation files for the given platform. Side effect: any expression experiment data files that use this platform will be deleted. Format details: There is a one-line header. The columns are:

1. Probe name
2. Gene symbol. Genes located at different genome locations are delimited by "|"; multiple genes at the same location are delimited by ",". Both can happen simultaneously.
3. Gene name, delimited as for the symbol except '$' is used instead of ','.
4. GO terms, delimited by '|'; multiple genes are not handled specially (for compatibility with ermineJ)
5. Gemma's gene ids, delimited by '|'
6. NCBI gene ids, delimited by '|'

Parameters:

inputAd - platform to process

overWrite - if true existing files will be clobbered

Throws:

IOException

generateAnnotationFile

int generateAnnotationFile(Writer writer,
                           Collection<Gene> genes)

Generate an annotation for a list of genes, instead of probes. The second column will contain the NCBI id, if available. Will generate the 'short' version.

Parameters:

writer - the writer

genes - genes

Returns:

code