Submitting Data to PMN

Please help us improve the PMN

We are grateful for any data or other information that users are willing to submit to the PMN, either to expand our coverage or to correct mistakes in our existing entries.
*Please note that incomplete information is also welcome; ANY partial information you can give us will help us to make the PMN a better resource for our users.

But, we request that you send references whenever possible.

Good reference formats:

Pubmed ID (can be found at the start of the last line of text for each entry on the “Summary” page view or in the bottom left corner of the "Abstract Plus" view)
DOI (often displayed at the journal site)
(Author. Year. Journal. Volume: Pages) or (Author, Year, Book Title, pages), etc.
Hyperlink to journal article
PDF of journal article
Hyperlink to another resource

There are four main options for contributing information

If you only want to describe something short in words, or make a brief correction, you can easily put this information into our Feedback Form Please include references if you have them
If you have your own ready-made datasets in Excel spreadsheets, pathway diagrams, compound structure files, etc. please send them using our Feedback Form or as an attachment using your favorite e-mail program to curator@plantcyc.org.

Good file formats:

Text / data:.doc, .pdf, .txt, .xls
Images:.gif, .jpg, .pdf, .ppt, .tiff
Compound structures:.cml, .inchi, .mol, SMILES

If you don’t see your file type here, please send it anyway; we will let you know if we can’t open it.

You can create a GoogleApps document, spreadsheet, or presentation and share it with a curator. Please invite one of the following:

Peifen (director): peifenz_at_gmail.com
Karthik (curator): akarthik_at_arabidopsis.org
Kate (curator): kadreher_at_tairgroup.org

We provide Excel-based forms to help you submit new information about or corrections for compounds, enzymes / reactions, and pathways. (If you need these forms in another format – e.g. Google spreadsheet, please let us know.)

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Filling in Data Submission / Correction Forms

Compound form

Enzyme / Reaction form

Pathway form

Please keep in mind the following while filling out the forms:

You do not need to fill in all the information. We have required columns and we ask you to enter information in each of them, but, if you are lacking a piece of information for one of the required columns, please send us the form anyway and we will try to fill in the missing data.
Please provide references whenever possible. Please help us to enter more information and enter it more reliably by providing a reference to each specific piece of data entered on the form, whenever possible. See good reference formats above.

*After you enter the detailed information for a reference once, please use the (Author Year) convention to refer back to the same reference, using a, b, etc., if necessary.

Save this form periodically and send the final form using our Feedback Form or as an attachment to curator@plantcyc.org using your normal mail client.
If you are submitting corrections, you only need to enter the new information that should replace existing mistakes. But, we welcome explanations of the inaccuracies present in our database.

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Compound Form

Columns A-H ask for basic information about the compound
Columns J-M ask for more detailed information

Basic Compound Information

Column A: Compound name (required)

Please give a common or scientific name for the compound that should be used as the primary name in a database entry.
*Please use the EXACT compound name found in our databases if you are suggesting a correction.

Column B: Submission or Correction (required)

Please select the appropriate term using the menu that is displayed when you click on the triangle to the right side of the cell.

Column C: Alternative compound names / synonyms / abbreviations

Please give as many names as you feel are appropriate or would be helpful. Please keep in mind that the program that allows overlays of metabolic data will be more successful if it has more synonyms to match.

Column D: Organism(s)
Please list all the specific organisms in which this compound has been shown to exist (with references if possible). If this compound is expected to be present in a whole group, such as the legumes, please add that (with a reference) We appreciate any comments that will allow us to distinguish between species in which the compound is predicted versus proven to be present.
Common names and scientific names are both welcome. We also welcome NCBI taxonomy codes.
Column E: IDs in other databases

We appreciate any and all IDs that we can use to link our compounds to other databases. Common ID sources include: PubChem, KEGG, CAS, ChEBI, but please send us any other type of ID as long as you inform us of the source.

Column F: Compound classification(s)

We do not currently use a formal chemical ontology to classify our compounds, so please give us any classification term that you use. You can assign more than one term to a compound, such as "secondary metabolite" and "terpenoid". The ChEBI site offers a good ontology if you need any suggestions.

Column G: Reference(s)/Link(s) to supporting evidence (required)

If you have additional references that have not been included in other columns, please provide them here. We welcome references for published data, but we will also gratefully accept links to lab websites, on-line databases, etc, where we can get more information about this compound.
See good reference formats above.

Column H: Comments / Summary

Please enter any free text you would like about the compound, including its interesting properties, biological relevance in plants, benefit (or harm) to humans and other organisms, etc. Please include any references you have that support the comments.

More Detailed Compound Information

Column J: Subcellular Localization

We welcome any information about the part(s) of the cell where your compound is made or stored. Please include any references you have that support the assignments.

Column K: Tissue/Organ Localization

We welcome any information about the part(s) of the plant where your compound is made or stored or transported through. Please include any references you have that support the assignments.

Column L: SMILES

Do you have the SMILES code for your compound on hand? If so, please just paste it in and we can readily create a structure.

Column M: Anything else you'd like to share . . .

If you have some piece of information that doesn't seem to fit anywhere else on the form, (e.g. an e-mail address for an expert in the field, a notification that this compound will show up in a pathway that you plan to submit soon, a personal greeting to the curator who might be working on the submission, etc.), please put it here.

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Enzyme / Reaction Form

Columns A-I ask for basic information about the enzyme
Columns J-Z ask for more detailed information

Basic Enzyme / Reaction Information

Column A: Enzyme name (required)

Please give us an enzyme name that describes its specific biochemical activty. We realize that it may be hard to include specific reactants or products in the enzyme name, but please do whenever possible.

Good names:

1-phosphatidylinositol-3-phosphate 5-kinase
12-oxophytodienoate reductase
.3-phosphoshikimate 1-carboxyvinyltransferase

Bad names:

ADH1
Hydroxylase 2

*Please use the EXACT enzyme name found in our databases if you are suggesting a correction.

Column B: Submission or Correction (required)

Please select the appropriate term using the menu that is displayed when you click on the triangle to the right side of the cell.

Column C: Synonym(s)

Please give as many names as you feel are appropriate or would be helpful. In this column we accept both "good" and "bad names." Please keep in mind that the Pathway tools program that the PMN uses to predict the metabolic pathways in new species will benefit from having additional names entered as synonyms.

Column D: Organism (Only 1) (required)
- Please list only one organism where the enzyme listed in Column A has been characterized per row. If you have information on orthologous enzymes, please enter that information in a separate row. If this enzyme is expected to be present in a number of different species, or in specific subgroups of species, please enter this information in the Comments / Summary Column (Column I)
- Common names and scientific names are both welcome. We also welcome NCBI taxonomy codes.
Column E: Reaction(s) catalyzed (required)
- Please list one reaction in each row and provide any references you may have to support these claims. We welcome reactions depicted as "A + B -> C + D"
- Please include any known co-factors (e.g. NADPH), but don't worry if this information is not known.
- You also do not need to balance an equation (for example, if a compound is glucosylated but the endogenous glucose donor is unknown).
- *Please include a full or partial EC number if you have this information
Column F: Reference(s)/Link(s) to supporting evidence (required)

If you have additional references that have not been included in other columns, please provide them here. We welcome references for published data, but we will also gratefully accept links to lab websites, on-line databases, etc, where we can get more information about this enzyme and/or reaction.
See good reference formats above.

Column G: Biochemical pathway(s)

If this reaction is part of one or more biochemical pathways, please enter this information. We welcome short answers such as "glycolysis" or "ornithine biosynthesis" but you can also submit a text description, such as, "an auxin conjugation reaction that generates an intermediate that can be stored or catabolized via further oxidation."

Column H: Gene / Protein sequence identifier or name
- To maximize the utility of the database, we want to provide links to protein and/or gene sequences whenever possible. Common sources include: NCBI, BRENDA, and UniProt. Please send us any other type of identifier as long as you inform us of the source (e.g. model organism database)
- You can also include "common" gene or protein names or abbreviations here, such as "ADH1."
- If you have sequence data at the nucleotide or protein level but no official IDs, you can enter the sequence information directly in Column W (protein) or Column X (DNA)
Column I: Comments / Summary

Please enter any free text you would like about the enzyme or reaction, including interesting properties, biological relevance in plants, the benefit (or harm) of the products to humans and other organisms, etc. Please include any references you have that support the comments.

More Detailed Enzyme / Reaction Information

Column K: Subcellular Localization

We welcome any information about the part(s) of the cell where your enzyme is located or your reaction occurs. Please include any references you have that support the assignments.

Column L: Tissue/Organ Localization

We welcome any information about the part(s) of the plant where your enzyme acts and/or is made or stored, and/or where the reaction occurs. Please include any references you have that support the assignments.

Column M: Molecular weight of monomer (kD)

Please give the weight in kD and indicate whether the weight is experimentally determined (with a reference) or calculated based on the protein sequence.

Column N: Part of enzyme complex?
- Please enter "Yes" if your enzyme is part of a heteromeric complex.
- Please enter "Yes" if your enzyme is part of a homomeric complex, including a homodimer.
- Please enter "No" if your enzyme acts as a strict monomer.
- Please enter "Unknown" for cases where there is no information or ambiguous information.
Column O: Enzyme complex description

If your enzyme is part of a complex, please describe both the identity and number of the subunits in the complex (with a reference). If there is only ambiguous data, e.g. that that enzyme A and B form a complex but the stoichiometry is not known, please give us that information, too.

Column P: Activator(s)

Please provide any information about substances known to activate the enzyme (with a reference). If you know whether the activator is physiologically relevant, and the mode of activation, please give us that information, too.

Column Q: Inhibitor(s)

Please provide any information about substances known to inhibit the enzyme (with a reference). If you know whether the inhibitor is physiologically relevant, and the mode of inhibition (e.g. allosteric, competitive), please give us that information, too.

Column R: Cofactor(s) or Prosthetic Group(s)

Please provide any information known about cofactors or prosthetic groups that are required for enzyme activity (with a reference).

Column S: Km

We welcome data concerning the Km of the enzyme. Please be sure to include the exact substrate used to measure the Km and include the units of measurement (with a reference). If the experiment was conducted at a particular pH, temperature, etc., this can be noted as well.

Column T: Temperature Optimum

We welcome data concerning the Temperature optimum of the enzyme. Please be sure to include the exact substrate used to measure the T(opt) (with a reference). If the experiment was conducted at a particular pH, this can be noted as well.

Column U: pH Optimum

We welcome data concerning the pH optimum of the enzyme. Please be sure to include the exact substrate used to measure the pH(opt) (with a reference). If the experiment was conducted at a particular temperature, this can be noted as well.

Column W: Protein Sequence

If you HAVE NOT entered an accession number of any kind in column H (Gene / Protein sequence identifier or name), but you do have access to the protein sequence, please paste it here. We welcome any additional data you can give. For example, is this protein prediction based on a predited gene model or is it based on an experimentally verified full-length cDNA sequence?

Column X: Coding Sequence
- If you HAVE NOT entered an accession number of any kind in column H (Gene / Protein sequence identifier or name), but you do have access to a DNA sequence, please paste it here.
- Please note that we are asking for a predicted coding region (no 5' UTR, no introns, no 3'UTR). We would just like a sequence that can be translated into a protein starting with the initiator methionine.
- We welcome any additional data you can give. For example, is this coding based on a predited gene model or is it based on an experimentally verified full-length cDNA sequence?
Column Z: Anything else you'd like to share . . .

If you have some piece of information that doesn't seem to fit anywhere else on the form, (e.g. an e-mail address for an expert in the field, a notification that this reaction will show up in a pathway that you plan to submit soon, a comment on the importance of the PMN to your work, etc.), please put it here.

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Pathway Form

*Please note that on this form, each step in the pathway should be entered as a separate row.
- You may enter multiple pathways on the same page, or you may use the additional duplicate sheets provided to enter each distinct pathway. Please let us know if you have submitted more than one pathway in your e-mail message.

- Since some of the information might be the same for each step of the pathway (e.g.Pathway synonym(s)), or for several steps of the pathway (e.g. sub-cellular localization). You are welcome to copy and paste the duplicated information or you can use the notation: "same as row X" where X is the number of the row where the duplicate data first appeared.

If you are submitting a correction to a pathway, you do not need to resubmit the parts of the pathway that are correct. Please just enter the new information that should replace the erroneous step(s).

Column A: Pathway name (required)

Please generate a name for the pathway. A good name typically includes the name of a final product, or class of products generated, and a descriptive word, such as "biosynthesis" or "degradation" to indicate the biological purpose of the pathway.

Column B: Submission or Correction (required)

Please select the appropriate term using the menu that is displayed when you click on the triangle to the right side of the cell.

Column C: Pathway synonym(s)

Please give any suggested synonyms for the pathway. For example, "auxin biosynthesis" could be a synonym for "IAA biosynthesis" that might be helpful to future users performing searches.

Column D: Organism(s)(required)
- Please list all the specific organisms in which this entire pathway has been shown to exist (with references if possible). If this pathway is expected to be present in a whole group, such as the legumes, please add that (with a reference) We appreciate any comments that will allow us to distinguish between species in which the pathway is predicted versus proven to be present.
- If some reactions are shared with other organisms that do not have this entire pathway, please do NOT include those organsims here. That information can be given using an enzyme form.
- Common names and scientific names are both welcome. We also welcome NCBI taxonomy codes.
Column E: Reaction (required)
- Please list one reaction in each row and provide any references you may have to support these claims. We welcome reactions depicted as "A + B -> C + D"
- Please include any known co-factors (e.g. NADPH), but don't worry if this information is not known.
- You also do not need to balance an equation (for example, if a compound is glucosylated but the endogenous glucose donor is unknown).
- *Please include a full or partial EC number if you have this information
- If you have more detailed information about this reaction, please fill out an an enzyme form and send it to us.
Column F: Enzyme(s)

Please list a name for the enzyme or enzymes that carry out the reaction and provide a reference if possible. You can add additional synonyms using a separate enzyme form.
*A gene or protein ID (from NCBI, TAIR, UniProt, etc.) for the enzyme would be very helpful.

Column G: Reference(s) / Link(s) to supporting evidence (required)

If you have additional references that have not been included in other columns, please provide them here. We welcome references for published data, but we will also gratefully accept links to lab websites, on-line databases, etc, where we can get more information about this pathway, enzyme and/or reaction.
See good reference formats above.

Column H: Subcellular Localization

We welcome any information about the part(s) of the cell where each step of the pathway occurs. Please include any references you have that support the assignments.

Column I: Tissue/Organ Localization

We welcome any information about the part(s) of the plant where the reaction occurs. Please include any references you have that support the assignments.

Column J: Comments / Summary
- Please enter any free text you would like about this particular step in the pathway, or about the pathway in general, including biological relevance of the pathway in plants, variants of the pathway found in other organisms, and the benefit (or harm) of the products of the pathway to humans and other organisms, etc.
- More information about particular steps or compounds can be entered using an enzyme / reaction form or a compound form.
- Please include any references you have that support the comments.
Column K: Anything else you'd like to share . . .

If you have some piece of information that doesn't seem to fit anywhere else on the form, (e.g. an e-mail address for an expert in the field, a notification that you plan to submit a related pathway found in other organisms soon, an invitation for PMN members to attend an upcoming meeting you're hosting, etc.), please put it here.

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Please contact us if you have any questions or check our FAQs page for answers to common questions.

Submitting Data to PMN

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