External Links
We encourage users of TAIR to submit external links associated to data objects found in TAIR. Submitted links will be added to the external link band on the object detail pages. Data objects accepted include: Loci, Clones, Genes, Polymorphisms, Genetic Markers, and Clone Ends. The locus example below would create a link on this locus detail page.
NOTE: If you want to link to ALL Arabidopsis LOCI and are using the AGI code (e.g. AT4G32520) as part of the variable for the URL, just send the External website name, base URL, and variable syntax to: curator@arabidopsis.org
If you would like to submit links for a subset of all the data objects found in TAIR, please submit your data in one of the following ways:
Option 1) Use a preformatted Excel spreadsheet. To submit your data, please download and complete the following excel spreadsheet. Note that examples and instructions have been included. Before submitting your data, review your entries to ensure that the data is correct. Send completed files to: curator@arabidopsis.org
Note: Macros must be enabled for this form to work properly. To allow the macros in this form to run, please change your macro security level to medium (recommended) or low. From the Tools menu, choose Macro, then Security. After you change the security level to medium or low, you will have to restart Excel.
Download: external_link_data_form.xls (CHANGE URL)
Option 2) Send tab-delimited data from any program. If you want to create your own file please follow the following format in submitting your data and send the files to: curator@arabidopsis.org. Please include the column headers as the first line in your files.
If you have any questions or suggestions, please contact us at: curator@arabidopsis.org
| Field | Description | Example |
|---|---|---|
| Object Name | The name of the object found in TAIR to be linked | AT4g32520 or ATDMC1.1 |
| Object Type | Type of object. Select from: Locus, Clone, Gene, Polymorphism, GeneticMarker, and CloneEnd | Locus or GeneticMarker |
| External Web Site - Name | Name of the website that the Base URL refers to | View AraCyc information |
| External Link - Base URL | Base rule for the URL. This is usually the portion of the external link URL before the question mark (?) | http://www.arabidopsis.org: 1555/ARA/NEW-IMAGE |
| External Link - Variable | Variable for the URL. This is usually the portion including and following the question mark (?) | ?type=REACTION-IN-PATHWAY& object=GLYOHMETRANS-RXN |
| Display Name | Name of the link to be displayed. For example, if the link is for an associated marker, you can provide the marker name. | formylTHF biosynthesis |
Gene Class Symbol Registration
What Constitutes a Gene Class Symbol?
Gene class symbols have been divided into two major categories (mutant phenotype and gene product) to facilitate curation. Mutant phenotype symbols should be used when a mutant is available and the symbol describes some aspect of the phenotype. Gene product symbols should be used regardless of the availability of a mutant when the symbol describes some aspect of gene structure or function. The use of organism specific prefixes such as At or Ath is discouraged as this is redundant and leads to a lot of genes named 'Arabidopsis thaliana X'.
Examples of Mutant Phenotype Symbols:
- ABA: ABA DEFICIENT
- AGE: AUXIN-RESPONSIVE GENE EXPRESSION
- EMB: EMBRYO DEFECTIVE
Examples of Gene Product Symbols:
- ADH: alcohol dehydrogenase
- AGL: AGAMOUS-like
- COR: cold regulated
Gene Structure Additions/Modifications
I have identified a new gene not in the current genome release. How can I add that information to TAIR?
Please contact TAIR to request a new locus identifier (i.e. AGI Locus code). Once you have the new identifier please contact TAIR to provide any information you have about the function or expression pattern of the new gene. If you are registered at TAIR, you can submit functional annotation information directly or register a new gene symbol. Registration is free.
I think the structure of a gene in the current annotation is incorrect. How can I correct it?
If you have sequence data that indicate the current annotation for a gene is incorrect, please contact TAIR to update the structure.
I think the functional annotation for a gene is incorrect. How can I correct it?
If you have data from a published article indicating that information about the expression, localization or biological role of a gene is incorrect, please contact TAIR. An example of an incorrect annotation would be if an article shows a gene to be expressed in the roots (but not shoots) and that same article is used as evidence for gene expression in shoots. If you have data that contradict other published works, we strongly encourage you to submit your own functional annotations and have them included in the gene record.
I know of published information on gene function that is missing from TAIR. How can I include it?
Please provide the missing gene function information using our online submission tool, GOAT. This form can be used by anyone to submit published data, whether you are an author of the publication or not. You will need to log in before filling out the form so that we can associate your name to the submission. If you experience difficulty or have information that will not fit within the form, please contact us.
Marker and Polymorphism Data
If you are submitting more than 150 entries, please e-mail curator@arabidopsis.org for additional instructions otherwise please submit your data by using the following preformatted spreadsheet:
Download: marker_polymorphism_data_form.xls (CHANGE URL)
Send completed marker files or any related questions to: curator@arabidopsis.org
Instructions on how to use the preformatted spreadsheet:
If available, always indicate the digest pattern/PCR length/base pair of Col-0 as a reference (not necessary for deletions/insertions).
Examples:
| Marker Name | Marker Type | Polymorphism Type | Polymorphism | Restriction Site | Ecotype |
|---|---|---|---|---|---|
| MARKER1 | CAPS | digest_pattern | 400;230 | 1 | Col-0 |
| MARKER1 | CAPS | digest_pattern | 630 | 0 | Hi-0 |
| MARKER2 | SNPlex | SNP | G | Col-0 | |
| MARKER2 | SNPlex | SNP | A | Hi-0 |
In the case where a marker or polymorphism is shared by several ecotypes, please list all ecotypes in the same row, as shown in this example:
| Marker Name | Marker Type | Polymorphism Type | Polymorphism | Ecotype |
|---|---|---|---|---|
| MARKER3 | SSLP | PCR_product_length | 165 | Col-0;Gr-6;Gu-0 |
| MARKER3 | SSLP | PCR_product_length | 150 | RLD;Wil-1;Wt-5 |
Fields indicated in blue are required. Fields marked with an asterisk (*) can contain multiple entries but these must be separated by a semicolon with no intervening spaces (e.g. Col-0;Ler-0). Note that examples have been included in the column headers; please retain headers as the first line in your files. You can find your Community ID and the Citation/Reference ID by using the links to our TAIR search pages provided in the template below.
If you have any questions or suggestions, please contact us at: curator@arabidopsis.org
| Field | Description | Values/Constraints | Example |
|---|---|---|---|
| Contact Person Name* | Last name,First name | No space between first and last names or between semicolon | Buschmann,Henrik |
| Contact Person Community ID* | unique identifier for a community member in TAIR. You must be registered to have a community ID | TAIR accession from TAIR Community Search | community:1035 |
| Contact Person E-mail Address | current email address | buschmann@gsf.de | |
| Marker/Polymorphism Name | PT1 or Salk_0228 | ||
| Alternative Names* | AtPT1 | ||
| Chromosome | The chromosome in which the marker/polymorphism is found | 1,2,3,4,5 or unknown | 5 |
| Genetic Marker Type | CAPS, SSLP, AFLP, RFLP, RAPD, SNPlex or Taqman | CAPS | |
| Polymorphism Type | Dependent on Marker Type | Digest_pattern (CAPS or RFLP), PCR_product_length (SSLP, AFLP, or RAPD), substitution, insertion, deletion | Digest_pattern |
| Polymorphism Lengths * | Length of digest or PCR product | numeric, in kb or bp | 0.12, 120 |
| Polymorphism Length Units | bp or kb | kb | |
| Flank Sequence Type | Required for all but RFLP submissions | PCR_primer or Flank | flank |
| Flank Sequence 1 | Required for all but RFLP submissions. The first PCR primer sequence | ATGGTGCCGTGACGT | |
| Flank Sequence 2 | Required for all but RFLP submissions. The second PCR primer sequence | AATTGGGTGTGCTAG | |
| Special Conditions | Indicate any special conditions required for marker detection | annealing temp 62C | |
| Restriction Enzyme Name* | Name of the restriction enzyme used to detect the polymorphism (required for CAPS, AFLP, or RFLP markers). | consult REBASE for standard enzyme name. | HindIII;EcoRV |
| Restriction Enzyme Number of sites* | Number of recognition sites for each restriction enzyme. The order of number of sites should match the order of restriction enzyme names in previous column. | numeric | 3 |
| Ecotype/Accession Name* | The ecotype which shows the specific polymorphism. If more than one ecotype shares a polymorphism, list all ecotypes. | Col-0 should always be shown as reference | Col-O;RLD;Ler |
| Accession Stock ID | For accessions that correspond to an ABRC stock, this is the stock ID number for that accession. | CS3455;CS3444 | |
| Polymorphic Sequence | Sequence of the polymorphic region for the given ecotype/accession | ATGTGGCCTCTT | |
| Map Position1 | Position of the SNP, insertion site, start position of 5' PCR primer/flanking sequence | 20215474 | |
| Map Position2 | End position of 3' PCR primer/flanking sequence | 26877049 | |
| TAIR Version | version of the TAIR genome assembly that your experiment is based on | TAIR9 | |
| Inheritance | The mode of inheritance of the polymorphism | recessive, dominant, co-dominant, semi-dominant, unknown | dominant |
| Marker/Polymorphism Citation/Reference_id | For a reference that describe the marker/polymorphism, this is the unique identifier in TAIR. For articles referring to the markers that are not yet in TAIR, please contact a curator to update this information into the database when the paper is published. | TAIR accession from TAIR Publication Search | publication:12344 |
Phenotypes
We accept phenotype data for all mapped and/or sequenced Arabidopsis mutants, including existing ABRC stocks, stocks from other stock centers, and lines that have not been deposited in a public repository. If you are submitting phenotype data for stocks not in ABRC we encourage you to consider also submitting the seed stock.
Please submit your phenotype data in one of the following ways:
Option 1) Use a preformatted Excel spreadsheet. To submit your data, please download and complete the following Excel spreadsheet. Examples are provided for each column. Send completed files to: curator@arabidopsis.org
Download: phenotype_data_form.xls (CHANGE LINK)
Option 2) Send tab-delimited data from any program. If you want to create your own file please follow the following format in submitting your data and send the files to: curator@arabidopsis.org. Please include the column headers as the first line in your files.
If you have any questions or suggestions, please contact us at: curator@arabidopsis.org
Description of column headers
| Field | Description |
|---|---|
| Contact Person | Please provide name and email of the contact person/corresponding author |
| Reference (Pubmed ID, DOI, or other format) | PMID: 18485063 - we prefer Pubmed ID, but the following format without Pubmed ID is OK too:Plant J (2008), 55: 798 |
| Allele Symbol / Polymorphism Name | For example: rpp3, rpp4(SALK_12345), atswc6(SAIL_1142_C03) |
| Accession | Example, Ws, Col-0 |
| Locus | If this polymorphism is an allele of a locus, enter the unique locus code here. Otherwise, leave empty. Example: AT4G32520 |
| Mutagen | EMS, X-rays, T-DNA insertion, transposon, fast neutron etc. |
| Mutation Site | Please describe the mutation site (3rd intron, 2nd exon, promoter, 3'UTR, 5'UTR etc). Please also give details of the mutation if known (for instance, contains a G to A subsitution at nucleotide position 123) |
| Genotype | Select from homozygous, heterozygous, hemizygous, and unknown. |
| Inheritance | Select from dominant, recessive, incompletely dominant, co-dominant, and unknown. |
| Allele Mode | Select from hypermorphic, hypomorphic, haplo-insufficient, antimorphic, gain-of-function, loss-of-function, and unknown. |
| Phenotype | Please provide a brief description of the mutant phenotype. Note: please specify if the phenotype is for double/triple mutants (for example, mop3/mop4). |
Protocols
TAIR encourages the research community to share their protocols. To submit a protocol to TAIR, send the protocol in one of the following formats.
Portable Document Format (PDF)
Microsoft Word Document (.doc)
Image (e.g. for powerpoint/photoshop images)- .gif and .jpg
Any text file .txt and .rtf
Along with the above file, please send in additional data following the format below to: curator@arabidopsis.org. Fields indicated in blue are required. Fields marked with an asterisk(*) can have more than one entry but the entries must be separated by a semicolon.
To find your Community ID and the Citation/Reference ID please follow the provided links to our TAIR search pages. If you have any questions or suggestions, please contact us at: curator@arabidopsis.org
| Field | Description | Values/Constraints | Example |
|---|---|---|---|
| Author(s)* | full name | 1000 character limit | Jerome Giraudat |
| Submitter's Community ID* | unique identifier for a community member in TAIR. You must be registered to have a community ID | TAIR accession from TAIR Community Search | community:4851 |
| Title | Title of the protocol | 500 character limit | Rapid RNA preparation |
| Description | brief text description | 1000 character limit | A method for rapidly preparing RNA from leaf tissue. |
| Publication/ Citation/ Reference_id | For a reference that describe the protocol, this is the unique identifier in TAIR. For articles referring to the markers that are not yet in TAIR, please contact a curator to update this information into the database when the paper is published. | TAIR accession from TAIR Publication Search | publication:501682410 |
| Usage keywords* | One or more keywords that describe the application(s) of the method (e.g. gene expression assay, protein-protein interaction assay). | separate multiple keywords with semicolons | gene expression assay |
| Method keywords* | use as many keywords as necessary to indicate the methods described in the protocol (e.g. mRNA isolation, cell fractionation). | separate multiple keywords with semicolons | Northern gel blot; RNA extraction |