Tutorials Overview

Understanding PMN Detail Pages

Each type of data (Pathway, Reaction, Enzyme, and Compound) in PMN databases has a detail page which can be accessed by the various search functions or through hyperlinks from other data detail pages. This section describes the Pathway Detail, Reaction Detail, Enzyme Detail, and Compound Detail pages.


Pathway Detail Page

Each pathway is represented on detail page in a zoomable graphical format along with links to information about the reactions, reactant and product compounds, enzymes and genes.

Pathway Diagram: Each pathway contains some of the following color-coded information.

  • Reactions are shown in blue lines, enzymes in yellow, genes in purple, compounds are red.
  • Green arrows indicate related pathways (e.g. pathways that feed into or depend upon the currently viewed pathway); click on the arrow to link to the pathway detail page for the related pathway.
  • Each of the data types in the pathway diagram are linked to their own detail pages.


Zoom Level Controls: The upper portion of the pathway detail page has two buttons which allow you to zoom in (or out) on the diagram.

  • Click on the "More Detail" button to zoom in and show more information about the pathway.
  • When the highest level of resolution is displayed, only the "Less Detail" button will be active.

Evidence: Each pathway is associated with an evidence code which indicates the type of data used to support the existence of the pathway. For more specific information, see the tutorial on evidence codes.

  • The evidence code icon is shown in the upper right hand corner of the pathway detail page.
  • More than one type of evidence may be associated with a pathway. Click on the icon to see details about the evidence and links to the citations where the supporting evidence was derived.

Superclasses: Pathways are classified into a hierarchy of superclasses.

  • The superclasses are hyperlinked to a page displaying all of the pathways contained in that superclass. You can navigate up the hierarchy to display similar pathways.

Species Data Available for: It is assumed that the entire pathway presented in the diagram is present in all of the species listed.

  • If there are variants on the pathway present in other organisms, these are listed by the Variants heading below the Summary.

Summary: Pathway detail page include a brief summary composed by the database curators.

References: For pathways that have been curated, the literature used as references are hyperlinked in this section.

  • Clicking on the citation will display the references used to curate the pathway.
  • Click on the reference to see details about the reference.

Unification Links: This section contains links to other databases containing related information.

  • The links depend on the type of data being displayed. For example, on a pathway detail page, there may be links to the same pathway in other data bases where you can find curated data about the same pathway in other specieses.

Pathway Evidence Glyph: The pathway evidence glyph is displayed only for pathways that have been computationally predicted. 

  • The glyph is a symbolic representation of the evidence supporting the individual reactions within a pathway.
  • **Even if a pathway diagram shows a flask icon (indicating the pathway is has experimental support), not all reactions in a pathway may be equally well supported.
  • The key below the glyph shows the correlation between the color codes and the evidence.

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Reaction Detail Page

The reaction detail pages can be accessed directly from the search results (e.g. when searching for a specific reaction) and from the list browser. They are also linked from related pathway, compound and enzyme detail pages.

  • To access specific reaction details from the pathway detail page, click on the blue reaction line (#426786) corresponding to the pathway of interest.

Superclasses: The reaction hierarchy represented in PMN databases is derived from the Enzyme Commission (EC) classification.

  • Each superclass is linked to a list of all of the reactions within the category. Users can browse the hierarchy to locate related reactions.

Pathways: Each reaction detail page lists all of the pathways in which the reaction is known or predicted to occur.

  • More than one isozyme can catalyze the reaction; there is currently no correlation between specific isozymes and the pathways in which they act.

Reaction Diagram: A diagram of the reaction is displayed in accordance with the direction of that reaction within a pathway where the substrate compounds are shown to the left of the equation and the product compounds to the right.

  • Clicking on the name or chemical structure of any compound will open the compound detail page.

Gene-Reaction Schematic: The gene-reaction schematic is a graphical representation of the relationship among sets of genes, enzymes and reactions.

  • The blue box on the left indicates the reaction (e.g. EC 3.1.3.11).
  • One or more yellow circles are linked to the reactions. These circles represent polypeptides and protein complexes.
  • Purple boxes which represent the genes that encode the proteins are linked to the yellow circles.
  • In the gene-reaction schematic provided above, the circles directly connect the genes to the reaction, indicating that the enzyme functions as a monomer.
  • In the gene-reaction schematic provided below catalyzed by a protein complex, each gene points to the same circle.


Unification Links: As with the pathway detail page, the unification links point to other databases that describe enzymes, reactions and proteins in the reaction.

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Enzyme Detail Page

The Enzyme detail pages can be accessed directly from the search results, from the list browser and from other detail pages.

  • From a pathway detail page, click on the enzyme (yellow text) name(#B07100), or click on the enzyme name on the reaction detail page.

Synonyms: Alternative names for the enzyme are displayed.

  • When searching for enzymes by name, the synonyms are also included in the search. Synonyms may be derived from the Enzyme Commissions enzyme nomenclature list.

Superclassess: As with the pathways, reactions and compounds, enzymes are ordered into a hierarchy which can be browsed from this section.

  • In general, reactions are classified according to EC hierarchy. Enzymes are not classified; most fall into the polypeptide category.

Comments: Comments include anything that the curators determine are useful information about the enzyme such as specific information about the isozymes, physico-chemical properties (e.g. pH, temperature optimum) and kinetic properties (e.g. Km).

  • Clicking on a citation in the Comments section brings you to the list of Citations at bottom of the Enzyme Detail page
  • Clicking on a hyperlinked citation in the list of Citations brings you to the PubMed abstract page for the reference, or directly to the journal providing the article.

Species: The species indicates the species(es) in which this enzyme is found.

Gene: The gene(s) that encode for the protein(s) that make up the enzyme are listed.
If an enzyme is multimeric and comprised of different protein products, all of the genes encoding the proteins will be listed here.

Gene-Reaction Schematic: This is the same diagram that is displayed on the reaction detail page.
In the diagram, the enzyme being displayed is indicated by the filled yellow circle.

Enzymatic reaction: The reaction(s) catalyzed by the enzyme are displayed, with the equation set up to reflect the observed directionality.

  • It is followed by a list of all the pathways in which this reaction occurs. This information can be useful in determining how changes in a given enzyme may affect metabolic pathways.
  • One enzyme may have multiple activities and catalyze more than one reaction. Each activity and the reaction catalyzed are listed on the enzyme detail page along with the evidence supporting the enzymatic activity.

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Compound Detail Page

Detailed information about substrate and product compounds can be accessed directly from the database search, or via links from other data detail pages.
Synonyms: Each compound may have one or more synonyms which are alternative names for the compound.

  • When searching for compounds in the database, all names including synonyms are included in the search.

Superclasses: Compounds are grouped into classes, which indicate their relationship to other classes of compounds.

  • Each superclass is hyperlinked to a list of compounds within that class. This list can be used to find similar compounds to any reactant or product.

Empirical formula and molecular weight: Basic information about the compound such as its empirical formula and molecular weight are shown here. This information can be useful for analyzing metabolomic data.

Structure: The structure of the compound is shown.

SMILES Profile: SMILES is widely used as a general-purpose chemical nomenclature and data exchange format.

  • This string can be used to find the same compound in other databases that use the SMILES format.

Unification Links: As with the other detail pages, links to similar or related information about the compound are listed here and hyperlinked to the corresponding database entry.

Participation in reactions

  • Reactions in which the compound is a reactant: For each compound, all of the reactions in which the compound is a reactant are listed here. Click on any of the reactions to see the reaction details.
  • Reactions in which the compound is a product: If a compound is a product of another reaction, the reaction is listed here and linked to the reaction detail page.
  • From these two lists it may be possible to identify other pathways that are likely to be affected by the concentration of a given compound. For example, a mutation that affects an enzyme reaction that generates a specific compound may ultimately affect the functioning of a pathway in which that compound is used as a reactant.

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

Assigning Evidence Codes in PMN

In order to assess quality of the data in the PMN databases, evidence codes are associated to the pathways and enzymes.

In the case of computationally derived pathways, color coding of the pathway glyph indicates how well supported individual reactions are.


Evidence Codes

All the databases in PMN use a controlled vocabulary of evidence codes. The three main classes (experimental, author statement and computational) of evidence are graphically represented on database detail pages.

The evidence codes are organized into an ontology that is available from the SRI Pathway Tools site.


Evidence codes for Pathways

An icon representing the type of evidence used to support the pathway is shown in the upper right hand corner of each pathway detail page. There are four kinds of icons:

  1. A flask (experimental evidence) (example)
  2. A book (a traceable author statement from the literature) (example)
  3. A computer (computational evidence) (example)
  4. A curator (inferred by curator) (example)

As an example, take a look at the pathway detail page for dTDP-L-rhamnose biosynthesis II in AraCyc.

  1. Go to the upper right hand corner of the pathway detail page. In this pathway there are two evidence icons displayed, a flask and a book. More than one evidence type can be used as support.
  • The computer represents evidence taken from computational evidence.
  • The flask indicates that evidence for the pathway was also based on experimental data from the literature.
  1. Point the mouse over one of the icons to see a brief explanation of the evidence code.
  2. Click on the evidence icon to display a definition of the evidence code and a link to the source of the evidence (e.g. the paper in which an experimental assay is described or where the author statement is found).
  3. In the window describing the specific support for the evidence code, clicking on the name of the publication takes you to the PubMed abstract or to the journal source of the article

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Evidence codes for enzymatic activities

Enzymes catalyzing reactions are also annotated with evidence codes. The same codes and icons are used for enzymes and pathways.

Using the same example pathway as before, GABA degradation, zoom in on the pathway using the 'more detail' button.

  • To learn more about 4-amino-butyrate transaminase, click on the name of this enzyme in the pathway diagram to go to the enzyme detail page.
  • This page lists all the activities catalyzed by the enzyme. Each of the activity catalyzed has an evidence icon in the upper right corner.
  • In this example, the first enzymatic activity (adenosylmethionine-8-amino-7-oxononanoate transaminase activity) has a book icon. Clicking on the icon reveals that this function is supported by a non-traceable author statement, and a link is provided to an abstract from a conference.
  • The second enzymatic activity (4-aminobutyrate transaminase activity) has a flask icon. Clicking on the icon reveals that there are two papers demonstrating this activity.

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Understanding the pathway evidence glyphs

The pathway evidence glyph on the pathway detail page for computationally-predicted pathways is another source of information about how well supported any pathway is. 

Note: Pathway glyphs are NOT present for pathways that have experimental, literature-based, or curator support.

In the pathway evidence glyph:

  • Each of the reactions in the pathway is color-coded to indicate how much is known about a given pathway.
    • Green: An enzyme catalyzing this reaction is present in this organism.
    • Black: No enzyme catalyzing this reaction has been identified in this organism.
    • Orange: The reaction and any enzyme that catalyzes it (if one has been identified) is unique to this pathway.
    • Pink: Represents spontaneous reactions, or lines that do not represent reactions (e.g. in polymerization pathways)

An example of a pathway evidence glyph is seen in the bottom of the Beta-Alanine Biosynthesis I detail page in AraCyc.

  • The top two reaction lines are green because enzymes predicted to perform these reactions are present in Arabidopsis.
  • The next two reactions in the middle branch of the pathway are black because no enzymes have been identified for these steps in Arabidopsis.
  • Orange lines also connect these four reactions, indicating that the reactions shown here are unique to the beta-alanine biosynthesis I pathway. (see note below).
  • Three of the reactions along the side branches are pink. Because they are spontanous reactions, no enzyme assignment will be made

The pathway evidence glyph helps to determine whether a computationally-predicted pathway should be retained in the database.

  • For example, if an enzyme catalyzes a reaction that is unique to a pathway and is found in the species, this may represent stronger evidence for the existence of that pathway compared to an enzyme that functions in multiple pathways.

The pathway evidence glyph helps to identify so-called "pathway holes" where the enzymes which catalyze specific reactions have not yet been identified.

  • Scientists aware of these holes may be able to design experiments to identify the missing components.

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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

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

  1. 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
  2. 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.

  1. 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
  1. We provide Excel-based forms to help you submit new information about or corrections for compoundsenzymes / 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:

  1. 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.
  2. 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.

  1. 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.
  2. 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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