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NCBI » GEO » Info » SOFT submission instructionsLogin

SOFT submission instructions

Starting in March 2024, GEO will no longer accept SOFT or MiNIML formats for data submission. Please use our metadata spreadsheet method for submission available on the Submitting data page.

• Overview
• SOFT format structure and content
  • Attribute guidelines
  • Platform data table guidelines
  • Sample data table guidelines
  • Raw data guidelines
• SOFT submission examples
• Batch updates in SOFT
• SOFT download

Overview Back to top

Simple Omnibus Format in Text (SOFT) is designed for rapid batch submission (and download) of data. SOFT is a simple line-based, plain text format, meaning that SOFT files may be readily generated from common spreadsheet and database applications. A single SOFT file can hold both data tables and accompanying descriptive information for multiple, concatenated Platforms, Samples, and/or Series records.

Affymetrix CHP files and supplementary data files like Affymetrix CEL or GenePix GPR scan files can also be provided - just bundle them together with the SOFT file into a.zip, .rar, or .tar archive using a program like WinZip at the time of submission.

SOFT format supports MIAME-compliant data submissions.

TIP: Use the 'command window' on your computer to concatenate multiple individual SOFT files into one large file for easy batch submission.
PC instructions: To open 'Command Prompt', click 'Start', click 'Run', type 'cmd', and then click 'OK'.
To concatenate individual files (fileA.txt, fileB.txt and fileC.txt) into one large file (largefile.txt), type 'copy fileA.txt + fileB.txt + fileC.txt largefile.txt'
Mac instructions: Open a 'Terminal' program window console.
To concatenate individual files (fileA.txt, fileB.txt and fileC.txt) into one large file (largefile.txt), type 'cat fileA.txt fileB.txt fileC.txt > largefile.txt'.

Examples of SOFT submission files and templates are available as guidelines for SOFT file structure and preparation.

Your final GEO records will look something as follows:

For almost all array data submissions, you will be asked to provide the following information:

A	Text description of the array or sequencer	Platform submission is not necessary if your array is already in GEO (e.g., Affymetrix chips). In this case, all you need is a reference to the Platform accession number (GPLxxx). Use the FIND PLATFORM tool to locate arrays.
B	Text tab-delimited table of the array template
C	Text description of the biological sample and protocols to which it was subjected
D	Text tab-delimited table of processed hybridization result or sequence counts	For Affymetrix data, a .CHP file may be supplied instead of a tab-delimited table using the !Sample_table attribute.
E	Raw data file, or processed sequence data file
F	Text description of the overall experiment
G	Tar archive of raw data files, or processed sequence data files

SOFT format structure and content Back to top

The following section explains the components and structure of a SOFT submission, as well as guidelines for content.

• Line-type characters: There are four different types of line that are recognized in SOFT. The presence of any one of three characters in the first character position in the line indicates three of the line types, and the absence of any of these indicates the fourth line type. The four line-type characters and descriptions of what they indicate are:

  Symbol	Description	Line type
  ^	caret lines	entity indicator line
  !	bang lines	entity attribute line
  #	hash lines	data table header description line
  n/a	data lines	data table row

  For simplicity, these lines are referred to as caret lines, bang lines, hash lines, and data lines, respectively.
• Label-value pairs: Label-value pairs are the generic way that lines are organized. Data lines are the only line types that are not organized in label-value pairs. Label-value pairs have the form:
  • [line-type character] [label] = [value]
• Entity types (caret lines): Entity type and its unique identifier are indicated as a label-value pair on the caret lines. The entity's unique ID is any string of characters different from any other entity ID within the document (i.e., locally unique). As described in the Overview submitters supply three entity types: PLATFORM, SAMPLE and SERIES.

  Entity type	Example entity indicator line
  Platform	^PLATFORM = my_array_name
  Sample	^SAMPLE = my_sample_name
  Series	^SERIES = my_series_name

• Attributes (bang lines): Entity attributes are contained in bang lines and immediately follow caret lines or other bang lines.

  The second column in the table indicates the 'number of allowed values' per attribute:

  • '1' indicates required, only one value allowed
  • '1 or more' indicates required, one or more values allowed
  • '0 or more' indicates not required, zero or more values allowed

  Several Sample attributes have _[n] where [n] indicates the channel number. For example, !Sample_label_ch[2]=Cy3 indicates that Cy3 was the label in one of the channels of a two-color experiment. If your experiment is single channel, _[n] may be omitted from the attribute.

  Human Genomic Data Submitted to Unrestricted-Access Repositories

  NIH-funded studies: If you plan to submit large-scale human genomic data, as defined by the NIH Genomic Data Sharing (GDS) Policy, to be maintained in an unrestricted-access NCBI database, NIH expects you to 1) submit an Institutional Certification to assure that the data submission and expectations defined in the NIH GDS Policy have been met, 2) register the study in NCBI BioProject regardless of where the data will ultimately reside (e.g., GenBank, SRA, GEO). If you have any questions about whether your research is subject to the NIH GDS Policy, please contact the relevant NIH Program Official and/or the Genomic Program Administrator. If you plan to submit genomic data from human specimens that would not be considered large-scale, it is your responsibility to ensure that the submitted information does not compromise participant privacy and is in accord with the original consent in addition to all applicable laws, regulations, and institutional policies.

  Non-NIH-funded studies: If your data are not NIH-funded, you are not required to comply with GDS policy but you must have the appropriate consent/permission to submit the data to a public database like GEO. GEO is not able to help interpret your consent forms, you should consult with your IRB on that. It is your responsibility to ensure that the submitted information does not compromise participant privacy and is in accord with the original consent in addition to all applicable laws, regulations, and institutional policies. If you do not have consent to make the data fully public in a database like GEO, you can apply to the NIH Office of Science Policy to find an NIH Institute that will sponsor your study in NCBI's dbGaP database. dbGaP has controlled access mechanisms and is an appropriate resource for hosting sensitive patient data. The sponsor would create a Data Access Request and Use Certification and define use restrictions for use in approving data access requests.

• Data table header description lines (hash lines): Data table header descriptions are contained in hash lines and immediately follow caret lines, bang lines, or other hash lines. Hash lines take the label-value pair form. Hash lines are used to provide a description of the headers named in the header line of the data table.

  A linking command may be given in the hash lines. Linking commands are used to automatically link individual cell contents. Linking commands may occur only in the value portion of the hash lines

  There are three linking commands currently defined, as follows:

  Command	Description	Example
  LINK_PRE	prefix string	LINK_PRE:"https://www.ncbi.nlm.nih.gov/nucleotide/"
  LINK_SUF	suffix string	LINK_SUF:".html"
  DELIMIT	delimiter string	DELIMIT:","

Platform data table guidelinesBack to top

• A Platform data table should lie between the !Platform_table_begin and !Platform_table_end attributes.
• Data tables must be in plain text (ASCII) tab-delimited format.
• It may not be necessary to submit a Platform record if your experiments are performed using commercial arrays (e.g., Affymetrix GeneChips). Official versions of many commercial array templates have already been deposited with GEO. To locate a commercial array, use the FIND PLATFORM tool and reference the appropriate Platform accession number (GPLxxx) in the !Sample_platform_id line. If you use a commercial array, but cannot locate its template in GEO, please proceed with Platform submission. If we can verify the content of the commercial Platform you submit, the contact information presented on that record will be edited from you to that of the vendor so that other users may easily locate and submit Sample data corresponding to that Platform.
• The Platform data table should only contain information that pertains to the content and design of the array. No expression measurement or hybridization intensity data should be included in the Platform table.
• Each row of the Platform table must be represented by its own unique identifier (ID). Keep in mind that the ID column you provide in your Platform table corresponds to the ID_REF column you provide in accompanying Sample data tables - there should be a 1:1 correspondence. Sample data tables should contain normalized data. This means, for example, if your normalization strategy requires taking the average of replicate array features, or removing control spots, your Platform table should reflect the condensed template. In this case, please e-mail or FTP the full array design file to us and we will attach it to your Platform record as a supplementary file - this ensures that your submission remains in compliance with MIAME standards.
• The Platform table must include meaningful, trackable, sequence identifiers (e.g. GenBank/RefSeq accessions, locus tags, clone IDs, oligo sequences, chromosome locations, etc - see table below for full list). This information enables other users to comprehensively interpret your data in compliance with MIAME standards, and allows GEO to retrieve up-to-date annotation for your Platform when incorporated into our downstream data query tools. References to in-house databases or top BLAST hits are not sufficient.
• The principal reason many journals require deposit of microarray data to a public repository is so that the scientific community has the ability to comprehensively evaluate or reanalyze the entire dataset. While we understand the various reasons and difficulties some researchers have with sharing data and array designs, the demand from users and journal editors together with our need to maintain a useful and transparent database has led to our policy of only accepting well-annotated datasets. If you have any questions or concerns regarding this issue, please e-mail us.

Standard Platform Headers

The first row in the Platform table must be a header line that identifies the content of each column. Column headers may be standard or non-standard. It is expected that at least one standard column (other than ID) will be supplied with each Platform submission.

In addition to these standard columns, your data table may include any number of non-standard columns. Examples of non-standard columns include array coordinate information, gene symbol or description, gene ontology terms, quality indicators, etc. Columns may appear in any order after the ID column. In this way, GEO is a flexible and open system, allowing you to provide all information necessary to thoroughly annotate your array.

Standard column headers and their content are as follows:

HEADER	CONTENT
ID	(Required) An identifier that unambiguously identifies each row on your Platform table. Each ID within a Platform table must be unique. This column heading should appear first and may be used only once in the data table. Keep in mind that the ID column you provide in your Platform data table corresponds with the ID_REF column you provide in accompanying Sample data tables. Sample data tables should contain normalized data. If your normalization strategy requires taking the average of replicate array features, your Platform should reflect the condensed template. In this case, please e-mail or FTP the full template file to us and we will attach it to your Platform record as a supplementary file.
SEQUENCE	The nucleotide sequence of each oligo, clone or PCR product.
GB_ACC	GenBank accession - identifies a biological sequence through the GenBank sequence accession number assigned to the sequence, or the representative GenBank or RefSeq accession number upon which your sequence was designed. It is recommended that you include the version number of the accessions upon which your sequences were designed (e.g., NM_022975.1 rather than NM_022975). This is particularly important for RefSeq accessions which are updated frequently. GenBank accessions representing the top BLAST hits for your sequences are not acceptable. Also, chromosome, genome and contig accession numbers are generally not acceptable as they are not specific enough to accurately identify the portion of the sequence printed on arrays (use GB_RANGE instead).
GB_LIST	GenBank accession list - as for GB_ACC, but allows more than one GenBank accession number to be presented. For example, your sequences may have GenBank accession numbers representing both the 5' and 3' ends of your clones. Multiple accession numbers should be separated using commas or spaces. Alternatively, more than one GB_ACC column may be supplied.
GB_RANGE	GenBank accession range - specifies a particular sequence position within a GenBank accession number. Use format ACCESSION.VERSION[start..end]. Useful for tiling arrays.
RANGE_GB	Use format ACCESSION.VERSION. Should be used in conjunction with RANGE_START and RANGE_END. Useful for tiling arrays.
RANGE_START	Use in conjunction with RANGE_GB. Indicates the start position (relative to the RANGE_GB accession). Useful for tiling arrays.
RANGE_END	Use in conjunction with RANGE_GB. Indicates the end position (relative to the RANGE_GB accession). Useful for tiling arrays.
RANGE_STRAND	Use in conjunction with RANGE_GB. Indicates the strand represented. Use + or - or empty. Useful for tiling arrays.
GI	GenBank identifier - as for GB_ACC, but specify the GenBank identifier number rather than the GenBank accession number.
GI_LIST	GenBank identifier list - as for GI, but allows more than one GenBank identifier to be presented. Multiple GIs should be separated using commas or spaces. Alternatively, more than one GI column may be supplied.
GI_RANGE	GenBank identifier range - specifies a particular sequence position on a GenBank identifier number. Use format GI[start..end].
CLONE_ID	Clone identifier - identifies a biological sequence through a standard clone identifier. Only CLONE_IDs that can be used to identify the sequence through an NCBI or other public-database query should be provided in this column. Examples include FlyBase IDs, RIKEN clone IDs and IMAGE clone numbers.
CLONE_ID_LIST	CLONE_ID list - as for CLONE_ID, but allows more than one clone identifier to be presented. Multiple Clone IDs should be separated using commas or spaces. Alternatively, more than one CLONE_ID column may be supplied.
ORF	Open reading frame designator - identifies a biological sequence through an experimentally or computationally derived open reading frame identifier. The ORF designator is intended to represent a known or predicted DNA coding region or locus_tag identified in NCBI's Entrez Genomes division. It may be appropriate to include a GENOME_ACC column to reference the GenBank accession from which the ORF names are derived.
ORF_LIST	ORF list - as for ORF, but allows more than one open reading frame designator to be presented. Multiple ORFs should be separated using commas or spaces. Alternatively, more than one ORF column may be supplied.
GENOME_ACC	Genome accession number - specifies the GenBank or RefSeq genome accession number from which ORF identifiers are derived. It is important to include the version number of the genome accession upon which your sequences were generated (e.g., NC_004721.1 rather than NC_004721) because updates to the genome sequence may render your ORF designations incorrect.
SNP_ID	SNP identifier - typically specifies a dbSNP refSNP ID with format rsXXXXXXXX.
SNP_ID_LIST	SNP identifier list - as for SNP_ID, but allows more than one SNP_ID to be presented. Multiple SNP_IDs should be separated using commas or spaces. Alternatively, more than one SNP_ID column may be supplied.
miRNA_ID	microRNA identifier - typically has format e.g., hsa-let-7a or MIRNLET7A2.
miRNA_ID_LIST	microRNA identifier list - as for miRNA_ID, but allows more than one miRNA_ID to be presented. Multiple miRNA_IDs should be separated using commas or spaces. Alternatively, more than one miRNA_ID column may be supplied.
SPOT_ID	Alternative spot identifier - use only when no identifier or sequence tracking information is available. This column is useful for designating control and empty features.
ORGANISM	The organism source of each feature on your array. This is most useful for when your array contains sequences derived from multiple organisms.
PT_ACC	Protein accession - identifies any GenBank or RefSeq protein accession number. Protein accession numbers should only be supplied for protein arrays. Nucleotide accession numbers should be supplied for nucleotide arrays.
PT_LIST	Protein accession list - as for PT_ACC, but allows more than one protein accession number to be presented. Multiple accession numbers should be separated using commas or spaces. Alternatively, more than one PT_ACC column may be supplied. Protein accession numbers should only be supplied for protein arrays. Nucleotide accession numbers should be supplied for nucleotide arrays.
PT_GI	Protein GenBank or RefSeq identifier. Protein identifiers should only be supplied for protein arrays or proteomic mass spectrometry Platforms. Nucleotide identifiers should be supplied for nucleotide arrays.
PT_GI_LIST	Protein identifier list - as for PT_GI, but allows more than one protein identifier to be presented. Multiple identifiers should be separated using commas or spaces. Alternatively, more than one PT_GI column may be supplied. Protein identifiers should only be supplied for protein arrays. Nucleotide identifiers should be supplied for nucleotide arrays.
SP_ACC	SwissProt accession. SwissProt accession numbers should only be supplied for protein arrays. Nucleotide accession numbers should be supplied for nucleotide arrays.
SP_LIST	SwissProt accession list - as for SP_ACC, but allows more than one SwissProt accession number to be presented. Multiple accession numbers should be separated using commas or spaces. Alternatively, more than one SP_ACC column may be supplied. SwissProt accession numbers should only be supplied for protein arrays. Nucleotide accession numbers should be supplied for nucleotide arrays.

Sample data table guidelinesBack to top

• A Sample data table should lie between the !Sample_table_begin and !Sample_table_end attributes (unless supplying Affymetrix CHP files or external text files, see !Sample_table attribute description).
• Data tables must be in plain text (ASCII) tab-delimited format (unless supplying Affymetrix CHP files, see !Sample_table attribute description).
• Normalized values should be included in the table.
• The Sample data table should only contain information that pertains to the quantification measurements. With the exception of the ID information, no annotation data that can be found on the reference Platform should be included in the Sample record.
• Complete data tables must be provided; it is not sufficient to present only significantly regulated genes. The principal reason many journals require deposit of microarray data to a public repository is so that the scientific community has the ability to comprehensively evaluate or reanalyze the entire dataset.
• If your hybridization data are available in a matrix format (data from multiple hybridizations are side by side in one table) consider submitting using the GEOarchive format.

Sample data table headers and content

The first row in the file must be a header line that identifies the content of each column. The two required columns are listed below. In addition to the required columns, submitters are encouraged to supply any number of auxiliary non-standard columns describing, for example, supporting measurements and calculations, quality evaluations or flags. Columns may appear in any order after the ID_REF column. In this way, GEO is a flexible and open system, allowing you to provide all information necessary to thoroughly describe your hybridization results.

• ID_REF: (Required) Identifier reference - these should match the unique identifiers given in the identifier (ID) column of the corresponding Platform data table.
• VALUE: (Required) These values should be the final, normalized quantification measurements that are comparable across rows and Samples, and preferably processed as described in any accompanying manuscript. Values that should be discarded (e.g., background higher than count, or otherwise flagged as 'bad') should either be left blank or labeled as "null".
  • For single channel data, this column should contain normalized (scaled) signal count data.
  • For dual channel data, this column should contain normalized log ratio data (preferably test/reference).

Raw data guidelinesBack to top

All submitters are now required to provide raw data with their submissions. Raw data facilitates the unambiguous interpretation of the data and potential verification of the conclusions as described in the MIAME guidelines. A raw data file typically represents the original scan file, for example, a GenePix GPR file or Affymetrix CEL file. Original TIFF image files may also be optionally supplied.

Raw data should be supplied in the form of external files and referenced within the SOFT file using the !Sample_supplementary_file attribute. Supplementary files should be bundled together with the SOFT file into a.zip, .rar, or .tar archive using a program like WinZip; do not include any sub-directories or sub-folders in the archive.
Alternatively, where possible, it is acceptable to include raw data columns alongside the normalized value data columns within the Sample data table. However, your submission will be enhanced by provision of the original quantified data files as these can often be read directly by data analysis software packages and may contain additional information that is useful for reanalysis.

SOFT submission example and template filesBack to top

The following examples (data tables truncated at 20 rows) represent valid GEO SOFT submissions:

• An example of a SOFT file containing a single Platform submission.
• An example of a SOFT file containing three dual channel Sample submissions.
• An example of a SOFT file containing a single Series submission.
• An example of a SOFT file containing a family (Platform, Samples and Series) submission.
• An example of a SOFT file containing three Affymetrix Samples and one Series submission.
• An example of a SOFT file containing three Affymetrix Samples and one Series submission referencing CHP files.

The following templates can be used to help prepare SOFT submissions:

• A template for a Platform submission.
• A template for a single channel Sample submission.
• A template for an Affymetrix Sample submission referencing a CHP file.
• A template for a dual channel Sample submission.
• A template for a Series submission.

Batch updates in SOFTBack to top

Batch updates are easy to perform in SOFT format - just include the attribute "!Sample_GEO_accession = GSMxxx" where GSMxxx indicates the accession number of the record to be updated (similarly, use !Platform_GEO_accession = GPLxxx, and !Series_GEO_accession = GSExxx). You can provide the entire SOFT record with the necessary revisions. Alternatively, you can simply provide the revised attributes and/or data table. Data table updates are 'all-or-nothing', e.g., to revise data in one column of a table, it is necessary to update the whole table.

Note that it is possible to perform SOFT updates on data that were submitted via any other submission route, such as the Web or GEOarchive. Likewise, it is possible to perform Web updates on individual records that were originally uploaded in SOFT format.

Submit your SOFT update file by selecting the 'SOFT' option on the Direct Deposit page. Make sure to check the 'Update' box. Successful updates will be reflected immediately on your GEO records.

The following examples (data tables, if any, truncated at 20 rows) represent valid SOFT update files:

• An example of a file updating Series attributes.
• An example of a file updating an attribute in multiple Samples.
• An example of a file updating data tables in multiple Samples.
• An example of a file updating data tables and attributes in multiple Samples.
• An example of a file updating Samples using complete SOFT records.

SOFT downloadBack to top

SOFT format is used not only for batch uploads and updates of data, but also for batch download. The only difference between SOFT input and output is a few additional attributes in the output, including:

_geo_accession
_status
_submission_date
_last_update_date
_row_count
_contact_name
_contact_email
_contact_institute
_contact_department
_contact_city
_contact_phone
_contact_fax
_contact_web_link
Sample_channel_count
Series_type

All GEO data are available for download in SOFT format from our anonymous FTP site