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This help document answers the following questions about the batch query tool:

• What can I use the MGI Batch Query to find?
• How do I use this tool?
• What are the accepted input identifier (ID) types?
• Does the input list have to be in any particular form?
• What does "Search all input types" accomplish?
• When would I constrain my search to a single input type?
• How many IDs can I enter at one time?
• Are there choices for how to view query results?
• Why can I select all the choices under Gene Attributes, but I'm limited to only one choice under Additional Information?
• Can I edit my original options and requery?
• How do I interpret results?
• MGI Batch Query results
• Mammalian Phenotype (MP) results
• Human Disease (OMIM) results
• Gene Expression results
• What do the acronyms in the Gene Ontology "code" column mean?
• What can I do to speed up my query?
• My query returned no results or No associated gene in one of the report columns. Why?
• Are there examples?

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What can I use the MGI Batch Query to find?

Use the MGI Batch Query to retrieve data about many MGI genes simultaneously. Currently, the tool retrieves;

• gene/marker attributes
  • nomenclature
  • genome location
  • Ensembl IDs
  • Entrez Gene IDs
  • VEGA IDs
• annotations
  • gene ontology terms
  • mammalian phenotype terms
  • gene expression tissue/assay data
  • MGI allele IDs
  • GenBank IDs
  • RefSeq IDs
  • RefSNP IDs
  • UniProt IDs

Future versions may include additional options.

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How do I use this tool?

Given a set of gene symbols or input identifiers (e.g. MGI accession, RefSNP, VEGA IDs) from a spreadsheet, you can:

• Copy and paste or upload a text file with a column of data into the Batch Query form. The column list can be mixed (e.g., gene symbols, synonyms, orthologs, IDs). You do not have to identify the type of input (e.g., marker ID, Entrez Gene ID) because the Batch Query tool detects the input type automatically.
• Specify the output in the MGI Batch Query Results (for example, nomenclature, genome location, Ensembl, Entrez Gene, or VEGA gene identifiers, gene ontology or mammalian phenotype IDs and codes, gene expression data, various other IDs), or Excel.
• View the results in either web (HTML), tab-delimited format.

You can also use the batch query to find duplications, ambiguities, and variations in data. You could check, for example, that an input list of MGI identifiers returns the same number of Ensembl, Entrez Gene, and VEGA IDs on different days or that switching the input and output IDs returns identical data. See Are there any examples? for additional ways you might use this query.

Note:

Be sure to remove any quotation marks or other non-alphanumeric characters from any list you enter or upload. The only valid delimiters are tab, comma/space, space, and new line.

Typing or pasting IDs

When typing or pasting IDs into the input box (you can copy and paste a column from an Excel spreadsheet):

1. Beneath Source, click the Enter Text tab.
2. Type or paste your list into the ID/Symbols List box. The Batch Query tool accepts space, tab, and newline-separated lists and removes any trailing commas.
3. Beside Type, either leave the default (Search all input types), or (when your list consists of a single input type and you want to make this distinction), click the arrow and select from the pulldown list. See When would I constrain my search to a single input type? for details.
4. In the Output area, click to select Gene Attributes, Additional Information, and Format to appear in the output report. (See Are there choices for how to view query results? for more information.)
5. Click Search.

Uploading a file:

1. If this is spreadsheet data, be sure to save the file in tab- or comma-delimited format.
2. In the Input column of the query form, leave the default (Search all input types) in the Type box, or click the arrow and choose a type from the list, if you wish to constrain the query. See When would I constrain my search to a single input type? for more details.
3. Beneath Source:, click the Upload File tab. A menu of choices appears.
4. Click Choose File and browse to locate your data. Once selected, the name of your file appears in the blank.
5. Beneath File Type and ID/Symbols column, check that the defaults (tab-delimited and 1) are correct for your uploaded file.
6. In the Output area, click to select Gene Attributes, Additional Information, and Format to appear in the output report. (See Are there choices for how to view query results? for more information.)
7. Click Search.

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What are the accepted input identifier (ID) types?

For a given query, your list can be either mixed or all of the same type. You can also enter (mouse) gene symbols, synonyms, or orthologs.

• When your input list consists of mixed ID types (for example, gene symbol, MGI ID, Entrez Gene ID, Homologene ID), use Search all input types (the default in the Type box). The following is an example of an input list requiring the use of the default:

  MGI:96677 
  Trp53 
  Pax-6 
  P53
  16590 
  ENSMUSG00000005672 
  OTTMUSG00000015949 
  247073 
  MI0000248 
  10379153
  

• When all the items on your input list are of the same type and you wish to constrain the query, click the arrow to the right of the Type box and select that type from the list. (See When would I constrain my search to a single input type? for more details.)

The following are representative examples for each type listed on the pulldown menu:

Input identifier type	Representative example
MGI Gene/Marker ID	MGI:96677
Current Symbols Only	Trp53 Pax6 D11Mit10
All Symbols/Synonyms/Orthologs (includes both current and old symbols)	Pax6 Pax-6 Trp53 P53
Entrez Gene ID	16590
Ensembl ID	ENSMUSG00000028530
VEGA ID	OTTMUSG00000015949
UniGene ID	247073
MiRBase ID	MI0000248
GenBank/RefSeq ID*	NM_001122899 AK033644 NP_666257
UniProt ID	P48356 A2AKJ2
GO (Gene Ontology)	GO:0019221
RefSNP ID	rs3021544
Probeset ID	10379153

*	GenBank IDs are for nucleotide sequences only. RefSeq IDs are for either nucleotide or protein sequences.

The following are additional types (not listed on the pulldown menu), followed by examples, of other types of IDs that the Batch Query recognizes:

Input identifier type	Representative example
BayGenomics	LST083
DoTS (Database Of Transcribed Sequences)	DT.529646
DCFI (Dana-Farber Cancer Institute)	TC1572427
EC (Enzyme Commission)	2.7.10.1
FHCRC (Fred Hutchinson Cancer Research Center)	FHCRC-GT-S15-11C1
Homologene	20151
Lexicon	OST128284
NIA Mouse Gene Index	U167412
PDB (Protein Data Bank)	1HU8

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Does the input list have to be in any particular form?

Yes.

• If there are spaces in any list entry (as for example, Dickie's small eye, a synonym for Pax6), you must enclose that entry in double quotation marks (i.e.,“Dickie's small eye”).
• The Batch Query tool accepts space, tab, and newline-separated lists and removes any trailing commas from such lists.

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What does "Search all input types" accomplish?

Since the Batch Query's default option is to search all input types, you do not have to identify what you enter or upload into the Batch Query. The tool determines whether they are of one type or a combination of IDs and or symbols. You may, however, select from the pulldown menu if you wish to constrain your query to a single type. See also When would I constrain my search to a single input type? below.

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When would I constrain my search to a single input type?

You may wish to select a single input type from the Type list when you want the Batch Query to return:

• Only current mouse gene symbols with MGI gene associations (for example, Acat1).
• Only current or former mouse symbols, synonyms, and orthologs with MGI gene associations.
• Results from one database and not another. Numerical identifiers (those without an alpha character), may recur in several databases (i.e., UniGene or Entrez Gene, and as an example, 12192).

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How many IDs can I enter at one time?

There is no limit to the number of identifiers that you can enter all at once, but there is a limit to how many numbers different browsers can present and there is a time constraint for very large files.

• Splitting long lists into sections speeds up return times. See the table under Why can I select all the choices under Gene Attributes, but I'm limited to only one choice under Additional Information? for examples of the amount of data that you can expect to return, depending on your input/output choices.
• Changing the default from Search all input types to the specific ID type is a good idea when you have a very large file containing one type of identifier (e.g., all symbols/synonyms/orthologs).

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Are there choices for how to view query results?

Yes. You can customize your results in three areas: Gene Attributes, Additional Information, and Format. Click to make your selections.

• Gene Attributes:
  You can retrieve gene/marker data for any/all of the following gene attributes or identifiers by clicking the boxes beside them. Each selected item adds one or more columns to the report.

  When you select...	the resulting columns contain....
  Nomenclature	symbol, name, marker type
  Genome Location	chromosome, start coordinate, end coordinate, strand, genome build
  Ensembl ID	Ensembl ID
  Entrez Gene ID	Entrez Gene ID
  VEGA ID	VEGA ID

• Additional Information:
  You can find data about objects associated with (or annotated to) genes. Select one of the following options per query. The default is not to return any of these data.
  

  When you select...	the resulting columns contain....
  Gene Ontology (GO)	ID, term, code NOT annotations do not appear in the results.
  Mammalian Phenotype Ontology (MP)	ID, term Normal annotations do not appear in the results. See How do I interpret Mammalian Phenotype (MP) results?
  Alleles	MGI allele identifier and allele symbols.
  Gene Expression	Anatomical structure (Theiler stage and tissue name), assay results (total number of times the structure was examined, number of times expression was detected in the structure, number of times expression was found to be absent in the structure). These numbers summarize results obtained from wild type and mutant specimens. The detected counts also include specimens for which detected = ambiguous or not specified (as well as present).
  RefSNP ID	RefSNP identifiers Results include RefSNPs within 2 KB of the gene/marker.
  GenBank/RefSeq ID	GenBank (nucleotide) or RefSeq (nucleotide or protein) sequence identifiers.
  UniProt ID	UniProt sequence identifiers.
  Human Disease (OMIM)	ID, term See How do I interpret Human Disease (OMIM) results?

• Format:
  You can view the output of your query results in your browser in several formats:
  • Web (HTML)
  • Tab-delimited text.
  • Excel
  The results are initially returned in web format and then you can choose to Export them in Tab-delimited text or spreadsheet formats.

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Why can I select all the choices under Gene Attributes, but I'm limited to only one choice under Additional Information?

The purpose of the single Additional information choice is to limit results to a reasonable size. There is quite an increase in the amount of data returned when you select an Additional Information category. For example, if you enter symbols for 9 paired box genes (your input list is Pax1, Pax2, Pax3, ... Pax9), and you select:

Nomenclature and ...	the MGI Batch Query returns...
Genome Location	9 rows, one for each gene, Pax1 - Pax9
UniProt ID	30+ matching rows
Gene Ontology (GO)	200+ matching rows
Mammalian Phenotype (MP)	650+ matching rows
Gene Expression	1400+ matching rows
RefSNP ID	~2900 matching rows

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Can I edit my original options and requery?

Yes, you can.

• If you want to edit a list or change output options:
1. When your results appear, click the banner at the top of the page (Click to modify search). (The banner title changes to Click to hide search.) The window that appears contains your original search criteria.
2. Edit the input list or change any Output options.
3. Click Search.
4. Repeat steps 1 and 2 until the desired results appear.
See Are there examples? for a sample of a query modification.
• If you want to upload a different file:
  1. When your results appear, click the banner at the top of the page (Click to modify search). (The banner title in changes to Click to Hide Search.) The window that appears contains your original search criteria.
  2. Click the Upload File tab and then the Choose File button.
  3. Select the appropriate file. See How do I use this tool? for more information about uploading files.

Notes:

• You can requery as many times as you like.
• Alternatively, click Reset to return to the original Batch Query form.

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How do I interpret results?

MGI Batch Query results

All Batch Query results appear in the form of a table in either web (HTML) format, or in tab-delimited text depending on your Output selection.

• A summary of your query parameters appears at the top of the page under You searched for.... It lists:
  • the total number of IDs/symbols you entered (or uploaded)
  • the input identifier type of those IDs (e.g., Search all input types, MGI Gene/Marker ID, Current Symbols Only, and so on)
  • your Output options (e.g., Nomenclature,Genome Location, UniProt ID, and so on)
  
  
• For each ID entered, at least one row is returned for that ID, its corresponding MGI gene/marker ID, plus columns for whichever attributes or additional information you selected (see Are there choices for how to view query results?).


• If a gene has more than one associated identifier, a row returns for each association (for example, there may be more than one Ensembl, Entrez Gene or VEGA ID; many GO or MP terms; lots of RefSNPs).


• Background row shading alternates by marker symbol. For example, if you were to enter Pax6 and Kit, all Pax6 associations would appear in one shading (e.g., light) and all Kit associations would appear in a contrast shading (e.g., dark).


• Entries in the Feature Type column (beneath Nomenclature) identify the category and/or subcategory of the marker (e.g., snoRNA Gene, QTL, Pseudogene, Complex/Cluster/Region, and so on.)


• When you select Gene Ontology (GO), three columns return: ID (with an entry such as GO:0005525), term (with an entry such as GTP binding), and Code (with an entry such as IEA. See Guide to GO Evidence Codes at the Gene Ontology website for the definitions).

Mammalian Phenotype (MP) results

The resulting list of Mammalian Phenotype Ontology terms associated with a gene is a combination of all terms associated with all mutant alleles of that gene.

• Mammalian Phenotype (MP) terms appear by gene.
• Each term describes a mouse phenotype with some mutation in that gene.
• The term does not necessarily imply that mutations in that gene contribute to or cause the phenotype.
• Analyzed mice may have causative mutations in other genes.
• Wide phenotypic variation exists due to homozygotes vs. heterozygotes and different strain backgrounds.

See also MGI Batch Query results for information on the other fields.

For detailed information, use the Phenotypes, Alleles & Disease Models Query Form to find your gene of interest and Mammalian Phenotype terms associated with specific genotypes and strains.

Human Disease (OMIM) results

Human Disease terms appear by gene, followed by an ID and the Mammalian Phenotype vocabulary term entry.

• Each term listed indicates that a mutant allele of this gene is involved in a mouse genotype used as a disease model.
• The term does not necessarily imply that mutations in that gene contribute to or cause the disease.
• Analyzed mice may have causative mutations in other genes.
• Wide variation exists due to homozygotes vs. heterozygotes and different strain backgrounds.

See also MGI Batch Query results for information on other fields.

For detailed information, use the Phenotypes, Alleles & Disease Models Query Form to find your gene of interest and view Human Disease terms as they are associated with specific allelic mutations and strains.

Gene Expression results

If there is expression data from a curated reference in the Gene Expression Database, the anatomical structure examined (listed by Theiler stage and structure name) appears, followed by columns indicating:

• the total number of assay results for this gene/tissue
• the number of positive assay results (+)
• the number of negative assay results (−).
• the detected counts also include specimens for which detected = ambiguous or not specified (as well as present).

Note: Present appears if expression is reported as detected but the author did not specify the level. Not specified is used when the authors do not report whether a gel band is present or absent. Ambiguous is used when the curators cannot discern from the authors’ description whether expression is present or absent.

See also MGI Batch Query results for information on the other fields.

Use the Genes and Markers Query Form to find a gene of interest and view additional expression results (e.g., Literature Summary, Data Summary, Theiler Stages, Assay Types, cDNA source data, External Resources).

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What do the acronyms in the Gene Ontology Code column mean?

See Guide to GO Evidence Codes at the Gene Ontology website.

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What can I do to speed up my query?

There are several options for speeding up a query.

1. Break the ID or symbol list into pieces and run several queries.
2. Eliminate Gene Attributes (remove the click next to Nomenclature) or select fewer of them (for example, only Ensembl ID, only Entrez Gene ID, or only VEGA ID).
3. Click None beneath Additional Information or select something other than RefSNP ID. If you want RefSNP IDs, using smaller input files will speed up the query.

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My query returned no results or No associated gene in one of the report columns. Why?

• No results are returned if you upload a data file and do not:
• specify the column containing your IDs or symbols correctly.
• select the correct file type (tab delimited or comma separated).
• No associated gene appears:
• In the row entry under MGI Gene/Marker ID, when the search does not find any annotations to/associations for that ID.
• For some (or all) entries, if a file is not tab delimited or comma separated. Hint: Save as tab delimited or comma separated and rerun the query.
• If you do not enclose any gene synonym (or identifiers) containing spaces in quotation marks.
     (e.g., change Dickie's small eye to "Dickie's small eye").

Note: If you get an error message before your query completes, try using a smaller list of IDs or selecting fewer output categories.

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Are there examples?

I want to see all phenotype annotations for two genes.

• From Gene Attributes, click any other data you want to see in the output report (or leave the default, Nomenclature).
• From Additional Information, click Human Disease.
• Change Input Type to Current Symbols Only (or leave the default, Search all input types).
• Type the gene symbols in the ID/Symbols List box.
• Click Search.

I want to add another item to an input list and see if there are different results depending on whether I use the default (Search all input types) or select an input type.

• Follow the instructions for the first example and click Modify when the results appear.
• Add an item to the list.
• Leave the default.
• Click Search again. The ID type is current symbol for some items and human synonym for others.
• Click Modify again.
• Don't edit the list but do change the Input Type to Current Symbols Only and click Search. All results are identified as current symbol.

I have a text file of MGI Marker IDs and I want corresponding GenBank/RefSeq IDs.

• Input box:
1. Next to Type, leave the default (Search all input types).
2. Beneath Source, click the Upload File tab. A menu appears.
3. Beneath File Type, check that the delimiter choice (tab-delimited or comma separated) and ID/Symbol Column number match the content of your text file.
4. Beneath ID/Symbols File, click Browse.
5. Locate and select your text file, then check that the filename that appears (beside Browse) is correct.


• Output box: Beneath Additional Information, click GenBank/RefSeqID.

Bottom of form: Click Search.

I want a list of MGI alleles for Entrez Gene IDs located in the third column of an Excel spreadsheet.

• In the Input box, next to Type, click the arrow and select Entrez Gene ID (or leave the default, Search all input types) on the pulldown list.
• In the output box, beneath Additional Information: click Alleles.
• In Excel, click the top of the column to select it, then Edit->Copy.
• In your browser, click inside the input box, and then Edit->Paste.
• In the Input box, click EntrezGene on the pulldown list (or leave the default, Search all input types).
• On the bottom of form, click Search.

I used the Genes and Markers Query Form and selected tab-delimited output for my results, and I now have a summary report with 67 matching items. How do I get a column of this data into the MGI Batch Query?

Note: The steps below do not work if you are using the Firefox browser. Check their website for a workaround or use a different browser for saving MGI Batch Query results in Excel.

• In the summary report:
1. Note the column number containing the data of interest.
2. Name the file and save the file.
3. Under Save as type:, select Text (Tab delimited).
• On the MGI Batch Query form, Input box:
1. Beneath Source, click Upload File, and then Browse to locate the file.
2. Click to select the File Type (tab-delimited), enter the column number (e.g., 6) and, if desired, make a selection beside from the list next to Type (e.g., MGI Gene/Marker ID) or leave the default (Search all input types).


• In the Output box, click the desired Gene Attributes and Additional Information options.
• On the bottom of the form, click Search.
• To re-query:
  1. Click Modify
  2. Change the Input and/or Output option(s).
  3. Click Search again.

Note: If your initial data are not in tab-delimited or comma-separated format, copy and paste the file into a spreadsheet, save it in one of those formats, and then use the MGI Batch Query to upload the desired column (be sure to identify the proper File Type and column).

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