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PubChem Deposition Gateway This site allows users to test data exchange for deposition of chemical structure and/or bioassay data into PubChem, and to provide data to be added to PubChem. Please obtain an account for login before you start. PubChem Deposition Gateway Accounts come in two types, Test and Deposition.
1. Getting Started 1.1 Logging into the PubChem Deposition Gateway
If you already have a "Test Account" and wish to proceed to putting data into PubChem, you should create a "Deposition Account". To make a "Deposition Account", press the "Create Deposition Account" button. 1.1.2 Existing User: If you already have an account, you may login to begin using the PubChem Deposition Gateway. Please enter your username in the text box labeled "Username:" and your password in the text box labeled "Password:", then push the "Log In" button below the previously mentioned text boxes. If you have forgotten your password, please click "Forgot Password?". You will be prompted for your "Username". An e-mail will be sent to the primary contact for that account with further instructions on how to proceed. 1.2 Creating a New Account Choosing an Account Type When creating a new account you have two types from which to choose:
1.2.1 Creating a Test Account A Test account allows a user to go through all the steps of uploading substance and/or bioassay data. To setup a Test account please follow three simple steps:
Test Account Information
Username Choose a username. If the username you request is taken, you will need to provide a different one. The username you provide must be at least six alphanumeric characters long and cannot contain spaces. Before your Test Account is activated for use, an e-mail will be sent to this address with further instructions. Notify About Submission Status ChangesPassword Choose an account password. You must type the same password in the text boxes "Password" and "Confirm Password". Please commit this password to memory, as you will need it every time you attempt to login to the PubChem Deposition Gateway. The password you provide must be at least six characters long and cannot be your username. First Name Your first name. Last Name Your last name. Additional Information Please type any additional information or notes in this text box. Data Transfer Agreement You must agree to the Data Transfer Agreement for this website, prior to receiving a PubChem Test Account. To agree, you must make sure the check box is checked. 1.2.2 Creating a Deposition Account A Deposition account allows a user to go through all the steps necessary to put substance and/or bioassay data into PubChem. To setup a Deposition Account please follow three simple steps:
After these three steps are complete and your information is reviewed and verified by a PubChem administrator, you may receive an e-mail notifying that you may login and begin using the PubChem Deposition Gateway. It is possible that you may be contacted by phone or e-mail by a PubChem administrator during this process. If you do not complete Step 3 within 24 hours of completing the first two steps, you may need to start again from Step 1. Multiple Users on One Account It is now possible to create one deposition account that contains multiple users, each having their own login and password.
Deposition Account Information
Username Choose a username. If the username you request is taken, you will need to provide a different one. The username you provide must be at least six alphanumeric characters long and cannot contain spaces. Before your Test Account is activated for use, we will send you an e-mail to this address with further instructions. Notify About Submission Status ChangesPassword Choose an account password. You must type the same password in the text boxes "Password" and "Confirm Password". Please commit this password to memory, as you will need it every time you attempt to login to the PubChem Deposition Gateway. The password you provide must be at least six characters long and cannot be your username. First Name Your first name. Last Name Your last name. Data Source The data source name used to refer to your substance collection. The name provided here should be as short as possible with an abbreviated acronym preferred. PubChem reserves the right to assign you a different data source name then the one you request. This data source name must be unique to PubChem. Once you have chosen this name, you will not be able to change it because it is used to track all of your data in PubChem. However, see the next item for how this can be accomplished. Data Source URL This should be the appropriate home page for people wanting more information on your organization. Company / Organization The Company or Organization name associated with this Deposition Account. Please include the division or group name, if appropriate. Job Title Your job title or position within the company or organization you represent. Phone Number The phone number where you and your organization can be reached. Street Address City State, Province, or Area ZIP Country Your physical or legal address to which correspondence may be sent. Additional Information Please type any additional information or notes in this text box. Data Transfer Agreement To apply for a deposition account, you must agree to the Data Transfer Agreement (html format) for this website as your data will be released to the public in PubChem, not like a test accounts, where data is accessible only to the depositor. To agree, you must make sure the "I agree" check box is checked. If your organization requires modifications to the Data Transfer Agreement, please contact NCBI help desk. 2. PubChem Deposition Gateway Uploading and managing depositions is fairly straightforward. First, you will need to familiarize yourself with the required file format documentation and review the PubChem Deposition Gateway help documentation. Essentially, the deposition process consists of uploading an appropriately formatted PubChem data file. The file contents are subjected to several stages of validation. After all validation checks are complete, an e-mail may be sent notifying you to review your submission. After your review, PubChem Deposition Gateway users with a Deposition Account may "Commit" their successfully validated data. Typically, your committed data will be made available in PubChem within two days. It is possible, however, that your committed data availability may be delayed, especially if you are notified that there is further action required on your behalf. The PubChem Deposition Gateway provides the means for you to manage and review your depositions. You may delete or review prior submissions. If you have a Deposition Account, you may also generate reports of prior submissions and retrieve the PubChem Substance identifiers (SID) for your successful depositions. When you enter the PubChem Deposition Gateway, you will see, immediately below the heading "PubChem Deposition Gateway", a navigation bar with various tabs and icons. You may click on the tab text or icons at anytime for navigation. These tabs are:
2.1 Home Tab Clicking the "Home" Tab gives you a screen listing short descriptions of the main activities from which you can choose:
2.2 Substances Tab Clicking the "Substances" Tab puts you onto the substance welcome page. 2.2.1 Substances > Welcome Tab The substance welcome page lists the main substance deposition activities from which you can choose:
2.2.2 Substances > New Tab Clicking the "New" Tab gives you a screen that allows you to upload a file into the PubChem Deposition Gateway. Prior to submitting any files, please review the following document describing the allowed format of files deposited. The format of the file you upload is expected to be in SD File format. Each substance in the SD file must have a unique registry ID in the appropriate SD field. A description of the allowed and required SD fields is available . For examples of suitable SD files for deposition, see this SD file. Press the "Browse..." button to select a file to upload to the PubChem Deposition Gateway. After selecting a file, provide comments in the "Comments:" text box that will help you track this deposition and, perhaps, provide useful information to the PubChem Deposition Gateway administrators. Please remember to press the "Submit" button after you have selected the appropriate file and provided necessary comments. When the file transfer is complete, you will be transferred to "Pending" displaying this submission. Please note that the file you upload to the PubChem Deposition Gateway may be compressed. Compressing your file may substantially reduce the time it takes to transfer your data. We support files compressed using the "gzip" compressor. Please note that we do not support "zip" or "bzip2" compressed files. When substances are deposited in PubChem, the depositor category will be assigned to all substances. Based on the depositor's category, users can expect to find additional category-specific information either on the PubChem substance summary page or on the depositor's site. The different categories and their descriptions are the following:
2.2.3 Substances > Pending Tab This tab gives you a list of your unfinished or recently added depositions to PubChem. A "Filter by Status" pull-down menu allows you to filter your submissions by multiple criteria. By default, all submissions, "Any Status", are shown. The other filter criteria are:
The pending submission table columns provide a summary of each deposition: IDThe pending submission table column headings can be used to sort the table. For example, clicking on "Started" will sort the table by date. Clicking the "Started" column header for a second time will reverse the order of the sort. Clicking on any row will put you in the Validation Summary View under a dynamically-created Pending <Submission-Id> Tab for the corresponding submission. 2.2.4 Substances > Pending <Submission-Id> Tab This tab is created when viewing any details for a particular submission in process. A. Submission Page Overview In this section the basic elements common to all views for a particular submission will be explained.
The progress meter shows a graphical timeline of your deposition. The main stages of the process are written above the meter. Each step may have multiple actions that must be completed before going on to the next step. The specific action that the system is undergoing at the moment is written immediately below the meter. The Summary information below the Progress Meter provides the Submitted timestamp of your upload and a summary of processing statistics. Critical statistics will be highlighted in red. The phases of the submission process, in order, are:
A. Validation Summary View Clicking the Validation Summary View provides a summary table of the unique message categories encountered during your deposition. The summary table columns are:
The column headings can be used to sort the table. For example, clicking on "Category" will sort the submission table by category. Clicking the "Category" column header a second time will reverse the order of the sort. Clicking on text in a row will transfer you to the Validation Details View filtered to show you only those records with that particular message category corresponding to the row you click. B. Validation Details View Clicking the Validation Details View provides a detailed list of all messages generated by the PubChem processing. The details table columns are:
To filter the details table by category of validation message, return to the Validation Summary View. To filter the details table for a substance, proceed to the List All View. Clicking on any text in a row will, typically, spawn a new browser window. Depending on the context of the message, this window will display different information. If the message is in the context of the records you uploaded, the window may display the SD file record number, a depiction image of the SD file record, and the uploaded SD file record, prefixed with the SD file line number. Alternately, if the message context refers to collision with a different submission, you will view the submission record from that deposition. C. List All View Clicking the List All View provides a summary view of the processed data records with counts of messages associated with that record. The processed records table allows for rapid navigation to particular records in your submission. The standardized table columns are:
Clicking on a row will transfer you to the PubChem Structure Preview View showing the substance record corresponding to the row you click. D. List Failed Standardization View In the case that you have substances which have failed standardization, an extra View will appear to isolate those failed substances. Clicking the List Failed Standardization View displays the same information as the List All View filtered for failed records only. Please note that if your substances do not have chemical information available, then it is expected and normal that they will "fail" Standardization. As with the List All View, clicking on a row will transfer you to the PubChem Structure Preview View showing the substance record corresponding to the row you click. E. PubChem Structure Preview View Clicking a particular substance record in the List All View or the List Failed Standardization View provides a summary view of complete individual substance records. The display of your substance closely resembles how the submitted data will appear in the PubChem Substance Summary CGI. The URL links are available on this page so you can test the links back to your website to verify that the URL's work as intended. Additionally, you can see how PubChem processing affects the data you have provided. The "Compound Displayed" pull-down menu allows you to toggle between the "PubChem" processed structure and the submitted "Deposited" chemical information, when such information is provided. If your substance has multiple components or is ionized, you may have additional views of unique component or neutralized forms of your substance. A navigation bar is available to step through your submitted substances:
F. History View Clicking the History View displays a detailed chronology of the processing phases for the submission. The history table columns are:
Action buttons
Clicking the Commit Button enables you to deposit the submission in PubChem. Your submission will be reviewed and, if approved, will be made public in the PubChem data system. Original File Icon Clicking the Original File Icon will allow you to download the data you submitted. Save Report Icon Clicking the Save Report Icon allows you to download a report file in CSV (comma separated value) format. Delete Icon Clicking the Delete Icon enables you to delete the submission you are currently viewing from the Deposition system only. This means the submission will have no affect on PubChem. 2.2.5 Substances > Deposited in PubChem Tab This tab gives you an archive list of your substance submissions which were successfully deposited in PubChem. Clicking on a row will take you to an Archived Submission Details View. From there you will be able to find specific substances and go to the corresponding entry in PubChem. The column headings can be used to sort the table. For example, clicking on the column "PC-Aid" will sort the table by that id. Clicking this column header a second time will reverse the order of the sort. ID 2.3 Assays Tab Clicking the "Assays" Tab puts you onto the assay welcome page. 2.3.1 Assays > Welcome Tab The assay welcome page lists the main assay deposition activities from which you can choose:
Choosing an Assay Action Perhaps the biggest change in how the Deposition Gateway handles assay depositions is that now you choose from four distinct assay actions whenever you want to affect your public data in PubChem. The first choice you must make is whether you want to create a new assay or modify one of your existing PubChem assays. If you want to modify a PubChem assay, you have three further choices of possible modifications:
2.3.2 Assays > New Tab
Clicking the "New" Tab is the starting point for creating a new biological assay deposition in the PubChem Deposition Gateway as a means of making your data public in PubChem. We will now have a brief overview of the assay deposition process. If you would like to skip to the specific explanation of the New Tab, click here. Understanding Basic Concepts Prior to depositing biological assay data into PubChem, it is important to understand the nomenclature we use so that you and we are referring to the same elements. Please read the following paragraph to make sure we are clear on a few terms: Substance, Assay Description, Assay Data, and Activity Summary. An Assay Description refers to the protocol and parameters of an assay, which can only be defined once. Assay Data are the actual results; as long as they follow the protocol of the Assay Description, Assay Data on new substances can be continually added. A Substance is the stuff being tested; typically it is what is in an assay plate well. A Substance can be a discrete chemical entity, e.g. aspirin, or a complex mixture, e.g. a plant extract. If you think the material in two assay plate wells is the same, we ask that you refer to it as the same Substance with a single Activity Summary. If you think material in two wells differ, please refer to them as two distinct Substances, hopefully with different chemical structures (or different mixtures), and surely with distinct Activity Summaries. It is of course very common to do replicates across different batches and salt forms of a Substance when you believe the salt form to be irrelevant to activity. Your data, however, must be reduced to a single Activity Summary per substance that is submitted as an integer value: "inactive" - 1, "active" - 2, or "inconclusive" - 3 (if there are indeed contradictory replicates). In this way, your results will be much more accessible and understandable to users through the various searching and graphing functions of the PubChem Bioassay system. New Assay Deposition Overview There are several steps in a new assay submission that must be followed sequentially to complete the process: (Submit Substances) > Create Description > Add Data > Approve > Deposit in PubChem
New Tab Description Click on the New tab under the Assays tab to begin uploading a bioassay into the NCBI PubChem Deposition Gateway. If you are returning to resume working on a new assay deposition, please look under the Pending tab to find it. Progress Meter Just under the rows of tabs in the middle of the page is the progress meter. The progress meter shows a graphical timeline of your deposition. The main stages of the process are written above the meter. Each step may have multiple actions that must be completed before going on to the next step. A brief explanation of each step can be found in the previous section. Input Assay Description Once you have read this section and are ready to input your description, begin by choosing your method of input: Prior to uploading or entering anything, please review this help document describing the allowed file formats. Once the bioassay has been deposited, all parts of it must pass an automated validation procedure without errors in order to be accepted into PubChem. If you need to make changes to your assay after deposition to PubChem, please refer to the "Modify" tab. An Assay Description defines the results you wish to report. You have the ability to provide a detailed description of the assay being performed. There are separate sections to provide a description, the protocol, comments, the activity outcome method, target data, annotated cross-references, result definitions, and restrictions on allowed data values. The description for a particular assay must be input before the corresponding data can be uploaded for the sake of validation. Once your assay is defined in PubChem with an initial set of data, you can continually add results tested on new substances for the same assay description by going to the "Modify" tab. Descriptions can be input by filling in the form on the webpage, by uploading an XML file or by using one of your existing PubChem assays as a template. You must define at least one result definition (TID). To see an example description, download and upload this example file. Fill in Form Enter each of the required and optional fields necessary to describe the assay (as described below) into the corresponding boxes. Once the boxes are completed, click on "Create" to enter the data or "Cancel" to start over. Upload Assay Description XML File Click on "Browse", choose the appropriate XML or gzipped XML file conforming to the PubChem standard for the PC-AssayDescription specification. Here is an example file. Use PubChem Assay as Template Choose one of your existing PubChem assays from the pulldown menu and click on "Load". This option is only for convenience; the assay you are creating will have no special link to the assay you chose for a template. You will be required to create a new RegID and Name for your new assay as with the other two input methods. Assay Description Fields The description of the assay defines the assay purpose and parameters. Fundamentally, the Assay Description defines the "columns" that are populated by the Assay Data "rows". Each "column" is assigned a result type identity (TID) in the Results Definition section. The Assay Data uploaded later must be reported in the same order as the TIDs defined in the Assay Description. Additionally, the Assay Data must be consistent with the Assay Description TID definitions. The description of an assay consists of nine parts: External Assay RegID, Name, Description, Protocol, Comments, Activity Outcome Method, Target Data, XRef Data and Results Definition. External Assay RegID Create your Description Once you have finished entering your description and verified that it is accurate, click on the "Create" button. If the system finds no errors with it, it will become a pending assay in the Deposition Gateway and you will be routed to a dynamically-created tab entitled "New assay assay-id" where the assay-id is an identifer to keep track of the assay while it is in the Deposition Gateway. To continue reading about the next step in the new assay deposition process, click on Add Data. Otherwise, we will now discuss the next Tab under the Assay Tab, the Modify Tab, which allows for various operations to existing PubChem assays. 2.3.3 Assays > Modify Tab Clicking on the "Modify" tab routes you to a Modify "Welcome" tab starting on a third row of tabs. 2.3.3.1 Assays > Modify > Welcome Tab The modify assay welcome page lists the three types of modifications you can make on one of your existing PubChem assays:
This tab is the starting point for the most common type of modification to an existing PubChem assay: adding or changing data results. With this mechanism you can add new data results, replace selected data results, or remove data results that are no longer valid. Note that any duplicated substance (SID/RegID) test results for a given assay (whether in the same data file or not) will be archived in PubChem. Only the most recent one will be available for searching. If you are returning to resume working on an Add/Change Data action, please look under the Pending tab to find it. To revoke test results please submit a csv file with the following format. If your intention is to revoke the actual substance, you must first revoke it from any assays where it is a test result, then revoke it from the Substancestab. Progress Meter Just under the rows of tabs in the middle of the page is the progress meter. The progress meter shows a graphical timeline of your deposition. The main steps of the process are written above the meter. These steps to Add/Change Data to a PubChem assay must be followed sequentially to complete the process: (Submit Substances) > Add Data > Approve > Deposit in PubChemEach step may have multiple actions that must be completed before going on to the next step. Click on a step for a brief explanation. Submit CSV Data File Pick the PubChem assay you wish to modify from the pull-down menu, click on "Browse" to choose your CSV data file, and click "Submit". Note that if you are already modifying this assay in a pending action, you will not be able to proceed. When it loads, an Add/Change Data <Assay-Id> Tab tab will be created for you for the next step of validating your data. Also note that for this action you can only view the description, but can not modify it. 2.3.3.3 Assays > Modify > Alter Description Tab This tab is the starting point for making small changes to your description. Typical examples of changes you can make here are fixing typographical errors in the Description/Protocol/Comments sections and adding XRef data, like a URL to your website. No data can be added in this action. You can not change the meaning or number of Results columns because such changes invalidate the assay's existing data. If you must do that, please see the Replace Assay tab. If you are returning to resume working on an Alter Description action, please look under the Pending tab to find it. For this action the revision of your PubChem assay will be incremented, but the version will remain unchanged. While in the Deposition Gateway, the pending assay will show a blank revision since it is being modified. Progress Meter Just under the rows of tabs in the middle of the page is the progress meter. The progress meter shows a graphical timeline of your deposition. The main steps of the process are written above the meter. These steps to Alter Description of a PubChem assay must be followed sequentially to complete the process: Edit Description > Approve > Deposit in PubChemEach step may have multiple actions that must be completed before going on to the next step. Click on a step for a brief explanation. Choose existing Description to modify Pick the PubChem assay you wish to modify from the pull-down menu and click "Load". Note that if you are already modifying this assay in a pending action, you will not be able to proceed. When it loads, an Alter Description <Assay-Id> Tab tab will be created for you for the next step of modifying your description. Remember that for this action you can not submit data. 2.3.3.4 Assays > Modify > Replace Assay Tab This tab is the starting point for making significant changes to your description. Typical examples of changes you make here are adding or removing a Results column or changing the data type of a Results column. For this action you must resubmit all of your data results along with your description change. If an existing data result is not resubmitted with this action, it will no longer be available in PubChem when the change is made public. Special note: This is a powerful action that should be used as a last resort. It is your responsibility to maintain consistency with what this assay currently means in PubChem. Think of PubChem users who expect that the existing data to this assay may grow in number, but will not change in definition. Even here you can not modify the External Assay RegID. If this is what you want to do, please consider creating a new assay. You can not use this action to only make small description changes, like adding a URL XRef. To do that please see the Alter Description tab. However, if you have a modification for a result's name or description which would invalidate existing PubChem test results, then this is the correct action. If you are returning to resume working on a Replace Assay action, please look under the Pending tab to find it. For this action the version of your PubChem assay will be incremented and the revision will be reset to zero. While in the Deposition Gateway, the pending assay will show a blank for both version and revision since they are being modified. Progress Meter Just under the rows of tabs in the middle of the page is the progress meter. The progress meter shows a graphical timeline of your deposition. The main steps of the process are written above the meter. These steps to Add/Change Data to a PubChem assay must be followed sequentially to complete the process: (Submit Substances) > Edit Description > Add Data > Approve > Deposit in PubChemEach step may have multiple actions that must be completed before going on to the next step. Click on a step for a brief explanation. Choose existing Description to modify Pick the PubChem assay you wish to modify from the pull-down menu and click "Load". Note that if you are already modifying this assay in a pending action, you will not be able to proceed. When it loads, a Replace Assay <Assay-Id> Tab tab will be created for you for the next step of modifying your description. Remember that this action will replace all of this assay's existing PubChem data. 2.3.4 Assays > Pending Tab This tab gives you a list of your unfinished or recently added depositions to PubChem. To resume working on a given assay (or simply to view its detailed information), click on one of the fields in its row. If you have not yet started on your desired assay operation, please choose from the New or Modify or tabs as appropriate. Please note that once your deposition has been successfully uploaded to PubChem, you will view it in PubChem and not in the Deposition Gateway. The successful deposition will remain listed here for a short time and then you can see a history of the operation under the Deposited in PubChem tab. If you'd like to make further modifications, you will choose it under the Modify tab in your list of PubChem assays. Also note that unfinished assay actions will be deleted from the Deposition Gateway after one month of inactivity. This will have no affect on PubChem and only means that you will need to re-enter your description and/or data as appropriate. The column headings can be used to sort the table. For example, clicking on the column "Action" will sort the table by the type of action. Clicking this column header a second time will reverse the order of the sort. Assay 2.3.5 Assays > <Assay-Action> <Assay-Id> Tab
Page Layout To Proceed box The To Proceed box on the left side below the tabs gives you a hint of what you must do next in order to advance your deposition to completion. Views The Views box on the lower left side lets you pick appropriate informational views of your deposition relevant to the current stage of the process. We will now go through a detailed explanation of the various views available. Some views are unique to one step of the process, some are unique to one of the four assay actions, and others are common (for example "View Description"). Please find the View you have questions about and read more about it.
This is the View where you upload your assay data file in CSV format. Click on "Browse" to choose your CSV data file, and click "Submit". If you are trying to find this view and already have data uploaded in your deposition, first click on Delete Data, then you will see this View. Also note that this View is not appropriate for the Alter description action as it does not allow data uploads. The data will be parsed and validated against the description information to find all relevant issues with the data. If there are any errors, you must resolve them before the data can be committed into PubChem. CSV formatted assay data The PubChem BioAssay Deposition System allows the use of CSV (Comma Separated Value) formatted data files for assay data deposition. The CSV column ordering for the first seven columns is fixed and must be exactly as documented below. Beyond that, there must be a column for each result (TID) defined in the description. The best way to get familiar with this format is to click on the "CSV Template" link (in the Add Data View only) to download a CSV template file using the Assay Description that you have already entered. This is a guide so that you can cut and paste your data into this CSV file while strictly maintaining the correct number of columns. For fields without data there will be nothing but consecutive commas. We also have an example CSV file with data. Your CSV file must either have no column headers or these automatically generated headers; any deviations will cause errors. Note that any duplicated substance (SID/RegID) test results for a given assay (whether in the same data file or not) will be archived in PubChem. Only the most recent one will be available for searching. Also note that at the moment the scheme whereby depositors are able to split their assay data into several data files and load them separately is not available. We hope to have a mechanism to load multiple files as a single deposition, but for now please combine them prior to uploading. The following fixed columns are expected in your CSV file. Don't put anything in optional fields for which you have no data. Column headers and their order in the data file(s) should exactly match names and order of the result definitions (TIDs). Column 1: PUBCHEM_SIDValidation Summary View Display issue categories related to the parsing and validation of your assay data. This view shows the general types of issues found in processing the data including errors, warnings and info. If errors are found, they must be resolved before the data will be accepted into PubChem. Warnings and info issues do not have to be resolved, but often indicate something that should be adjusted. NDepositors are able to modify/change their uploaded CSV file by uploading a new one. Validation Details View Display all instances of issues related to the parsing and validation of your assay data. This view lists a line for each issue found in processing the data including errors, warnings and info. This list can be very large in some cases, so it is best to begin with the Validation Summary View. If errors are found, they must be resolved before the data will be accepted into PubChem. Warnings and info issues do not have to be resolved, but often indicate something that should be adjusted. N View Description View Review the description of a pending assay in read-only format. To see the description in machine-readable format, click on the Export Files Pulldown and choose either the XML or ASN format (if you have data loaded, those options will also include the data in the file). If you want to edit the description, you must first delete any uploaded data, then go to the Edit Description View. If you want to remove the assay from the Deposition Gateway (no affect on PubChem), again make sure any uploaded data is deleted, then click the Delete Session Icon. For more information on specific assay description fields, see here. Edit Description View Make modifications to the description of a pending assay. This view is only available when any uploaded data has been deleted from your pending deposition. This view is never available for the Add/Change data action. Restrictions on what you can edit apply in particular for the Alter Description action, but in no case can you edit the External Assay RegID. For more information on specific assay description fields, see here. History View This view displays a detailed chronology of the processing steps for the pending assay action. This history is only for the current pending action and does not include previous actions you have committed to PubChem for the same PubChem AID. To see an overall history of the actions you have committed to PubChem for all of your assays, click on the Deposited in PubChem tab. The columns are: N View Data View Display uploaded assay data in read-only format. Of course this view is only appropriate if you have uploaded an assay data file. If that file has passed the first phase of the Add Data step, which is "Data Parsing", then you will see your data file parsed into columns with the corresponding headers at the top and the data displayed on multiple pages as necessary. The first column, "N", numbers the records and the next seven columns are the predefined columns specified earlier for the CSV format. The second column, SID, is the PubChem Substance identifier. Each SID number links back to the appropriate PubChem substance summary page. The remaining columns, TID1..N, correspond to the Results Definitions as shown in the View Description View. If you have failed "Data Validation", the second phase of the Add Data step, it is useful to look at this parsing and make sure it is what you intended. Perhaps you forgot a comma somewhere in your CSV file and your data is lined up with the wrong column headers. Note that if your file could not get past the first phase of "Data Parsing", then an attempt will be made to show the text of your file as is. For convenience we will add line numbers, "N", and then show the text under the header "Unparsed Text". If you would like to change something in your data file, first click on Delete Data, and then resubmit your modified file. If you would like to download your original CSV file or the machine-readable (XML/ASN) file generated from it, click on the Export Files Pulldown. Assay Action buttons
Clicking the Export Files Pulldown allows you to download various files. If you have submitted a CSV data file, you can download it or the parsed XML or ASN file that we create from it. You can also download the description only as an XML or ASN file. Delete Data Icon Clicking the Delete Data Icon enables you to delete the attached data file so that you can resubmit it or go backwards to edit your description or delete the action from the Deposition System. The Delete Data Icon is required for going backwards in the deposition process. Also, remember that deleting here refers to the Deposition system only; this action will have no affect on PubChem. Delete Session Icon Clicking the Delete Session Icon enables you to delete the current assay action from the Deposition System's pending list. This action will have no affect on assays in PubChem. Commit Button Clicking the Commit Button enables you to deposit the submission in PubChem. Your submission will be reviewed and, if approved, will be made public in the PubChem data system. 2.3.6 Assays > Deposited in PubChem Tab This tab gives you a history of all assay actions taken by the Deposition Gateway which successfully affected PubChem. Each action will be listed on one line. This means that for one PubChem assay it will have a line for when the assay was first created. It could have additional lines for when it was modified, either by adding more data or by modifiying its description. Clicking on a row will take you to the corresponding entry in PubChem. The column headings can be used to sort the table. For example, clicking on the column "PC-Aid" will sort the table by that id. Clicking this column header a second time will reverse the order of the sort. PC-AID 2.4 Account Info Tab This tab allows you to manage your account preferences and contact information. It creates a second row of the following tabs:
Multiple Users on One Account It is now possible to create one deposition account that contains multiple users, each having their own login and password. For an overview of the process, click here. Views The Views box on the lower left side lets you pick appropriate views of your account information relevant to the second-row tab that you are under. A detailed explanation of the various views available are discussed under the sections explaining each of the second-row tabs. To read more, please find the View you have questions about. 2.4.1 Account Info > Account Tab This tab puts you by default into the "View Account" View that allows you to manage your account information. For an explanation of individual fields under this tab, please see the appropriate test or deposition account description. View Account View This View gives you read-only access to your account information. Edit Account View This View allows you to modify some of your account information. If there is information you need to update, but the field cannot be edited, please contact the NCBI help desk. After you make all desired changes, be sure to press the "Update" button to commit your changes. 2.4.2 Account Info > Contacts Tab The Contacts Tab is only available for the primary user of a deposition account (i.e. the user who first opened the account for your data source). List Contacts View This view displays a summary of contact information for the "Primary Contact" (primary user) and below that one row for each of the "Additional Contacts". Clicking on the Primary Contact row takes you back to the Account tab. Clicking on a row of the Additional Contacts takes you to the View Contact view for that contact. The contacts listed include information from the following columns:
Add Contact View This view allows you to add a contact for this deposition account. Please fill in all fields as completely as possible. You must fill in fields with a red "*". Allow to login independently The first checkbox on the "Add Contact" form determines whether this new contact will be able to login independent of the primary user.
View Contact View This View gives you read-only access to the contact's account information. Individual fields are defined just like the primary deposition account. Edit Contact View This View allows you to modify the contact's account information. Note that once a contact with independent login has been added, you should be very careful to make any changes to their account information. Each user can make his own changes. Also note that the primary user can change a contact's password, but can not view it. Individual fields are defined just like the primary deposition account. Please note: If you uncheck the Allow Login box for a contact that has an existing login, both his login and password will be lost. 2.4.3 Account Info > Preferences Tab This tab displays a few preferences that you can review and revise. As with the other tabs, if you wish to make modifications, click on the "Edit Preferences" View on the left. Data Source Description Terms One of the more powerful aspects of PubChem and its background search engine, Entrez, is its categorization and linking of related data. This section offers a list of terms to categorize the type of data you provide to PubChem. Please choose at least one term (more than one is ok too). PubChem users looking only for toxicology data, for example, will be able to limit their search to those data sources, thereby making your data more accessible. Auto-Confirm Substance FTP Depositions This checkbox applies only to substance depositions made via FTP. If checked, all such depositions will be automatically confirmed on your end if they pass validation. This means you will not have to click on the "Commit" button on the user interface in such a case. The submission will still need to be reviewed and approved by a PubChem curator, but one manual step will be eliminated. View Preferences View This View gives you read-only access to your preferences. Edit Preferences View This View allows you to modify your preferences. After you make all desired changes, be sure to press the "Update" button to commit your changes. Add Icon Clicking the Add Icon allows you to add a secondary contact for a deposition account. Please fill in all fields as completely as is possible. You must fill in all fields with a red "*". After completing the contact information form, please push the "Register" button. 2.5 Navigation Icons 2.5.1 Check Mark Icon Clicking the "Checkmark" icon in the Main Navigation Bar spawns a new web browser window and displays the PubChem Deposition Agreement in PDF format, requires Adobe Acrobat Reader to view. PubChem Depositors must (electronically) sign this agreement prior to adding any data to PubChem. 2.5.2 Movie Man Icon Clicking the "Movie Man" icon in the Main Navigation Bar spawns a new web browser window and plays a movie, requires Macromedia Flash Player plug-in to view, within that window demonstrating the use of the PubChem deposition system. 2.5.3 Question Mark Icon Clicking the "Question Mark" icon in the Main Navigation Bar spawns a new web browser window and displays the PubChem Deposition Gateway help document. You can learn about the various features of the deposition system by exploring this document. 2.5.4 Person Icon Clicking the "Person" icon in the Main Navigation Bar prompts you if you would like to log out of the PubChem Deposition Gateway. 3. PubChem Deposition Gateway FAQ's Q: I uploaded my file, now what? A: The PubChem Deposition Gateway will parse and validate the data you submitted. You can watch this process proceed, or you may submit another file or logout and come back later. When this processing is complete, as denoted by the submission status bar or by receipt of an e-mail, you may want to review the submission. If you have a Test Account, and the submission proceeded without error, you have successfully tested your data and can be assured that your data is ready for use with the PubChem Deposition System. If you have a Deposition Account, and the submission proceeded without errors, you may commit your data to PubChem by pressing the "Commit" button. Q: Can I supply an additional datasource URL as well as my datasource URL? Can I supply an additional substance URL as well as my substance URL? A: You have two URL's per substance. One URL is associated with your data source name and the other is associated with your unique registry ID. Beyond that, you would need to use the Entrez "link-out" mechanism that can "piggy-back" URL's on your (or anyone's) substances. Q: Can I supply multiple lines of additional searchable text per Substance? A: All additional information should be put in the comments ("PUBCHEM_SUBSTANCE_COMMENT") section of the SD file. You can have as many lines as you need there. You could also put URL's there, too. Q: If I have new information available, do I need to re-deposit the complete substance record including the new information or can I just deposit the new information? A: You need to re-deposit the complete record, including the new information, using the same registry ID. This will "replace" the old data. [Actually, it will version the record and only the new version will be indexed, searchable, etc.] Q: If a substance ceases to be part of my data, how do I delete the record in PubChem? A: You will need to re-deposit the record such that it contains only the registry ID and a revoke tag ("PUBCHEM_REVOKE_SUBSTANCE"). We suggest that you provide a comment (a line of text) with this SD tag to designate why you revoked the record. For example, "Substance was removed 2005-05-21". Q: If I find a mistake in my PubChem Substance record, is it better to update or remove my substance? A: The best way is to "update" the substance record. Q: After I get a deposition account, is my test account still active? Can I still use it to test submissions? A: Yes, the test account is still active. You may continue to use that account for testing. Please be advised that test accounts will not allow you to deposit data into PubChem. Deposition accounts will allow you to deposit data into PubChem, after processing has successfully completed. Q: We have various flags "nucleophile", "electrophile", "yuck" that we are starting to attach to molecules in our deposition. We'd like to send that data to PubChem in the most useful way possible. We think of them as "properties". What is the best way to do that? A: The substance/compound properties you mentioned above will go to PubChem's "Comment". You can simply put them under sd tag <PUBCHEM_SUBSTANCE_COMMENT>. Q: If we have CAS registry numbers, is it best to put them in <PUBCHEM_GENERIC_REGISTRY_NAME> or <PUBCHEM_SUBSTANCE_SYNONYM> ? Does it matter? A: The PubChem original design let user to put all "Registry" items under <PUBCHEM_GENERIC_REGISTRY_NAME>. Since many depositors already put the CAS numbers under their own synonyms field, those CAS numbers will automatically go to the <PUBCHEM_SUBSTANCE_SYNONYM>. So it doesen't matter and up to you to put them in which field. Q: We are starting to collect annotations of compounds e.g. inhibits enzyme XYZ with Ki=10uM using a spetrophotometric assay. Also, we annotate compounds as being aggregators (non specific inhibitors) at a particular concentration. This is starting to sound like something that overlaps with the PubChem Assay database. So far we don't have a lot of data to upload, but that may soon change. Can you advise us on the best way to send this data to you? A: Yes. You are right. Such bio-data related to your substance will go to PubChem BioAssay database. Q: From time to time, compounds become depleted at various suppliers. We would like to either A. indicate in the comment record that this supplier's stock is depleted. OR B. remove a supplier from the comment record completely. A: Once you update your record, we will archive all old version content. We recommend you indicate in your comment. Q: Is the only way to do this to upload the full SD record again, overwriting the previous one? I think this is true, but wanted to make sure. A: Yes. Q: Do you want compounds that are depleted in PubChem? I figure the answer is yes, because what you are really looking for is maximum coverage of chemical space. So I'm thinking, why don't you just run a combichem/de novo design program to enumerate millions of molecules, and then load them into PubChem? Obviously, just chemical space isn't what you're after. Can you help me understand the PubChem perspective on this issue? A: PubChem substance database is depositors based. Every deposited substance will be assigned an SID. PubChem compound database is a non-redundant, structure unique database. Every compound in the database has a unique CID. If substance(s) linked with this compound become depleted, the compound will be deprecated/suppressed. We will keep all deprecated/suppressed compounds archived, and compounds will be never depleted. 4. FTP Depositions & FAQ FTP-based deposition provides a path for completely automated data upload into PubChem. If you have a large amount of data to be uploaded into PubChem or if you update your data on a daily or weekly basis, you may be a good candidate to use the PubChem FTP deposition method. To get started with FTP-based depositions, you must:
Substance-based FTP Depositions To deposit data for a Substance deposition via FTP, you must: Assay-based FTP Depositions Bioassay data depositions can be initiated via FTP in much the same way that substance depositions can, but for assays you must additionally specify the type of assay deposition operation. To begin, follow the same three-step setup procedure as described for substance FTP depositions. Note that you use the same FTP account for depositing either substance or assay data. Once your FTP account is setup, you should have the following directory structure under your top level directory:
You must decide which of the four types of assay operations you want to perform and place your file to be deposited into the appropriate directory highlighted above. You should be familiar with performing these assay deposition operations before trying them with FTP. For more information on them, see here. Assay FTP Deposition File Format To upload any kind of assay data or description changes, a single XML or ASN.1 file is required. This file must adhere to the specification for assays and be filled out as appropriate. Search in the specification file (XML Schema, ASN.1) for the tag PC-AssayContainer; this will always be the outermost container for your assay, whether it contains description and data or only description. You can find examples of such XML files from the PubChem public FTP site of bioassays. For assay deposition path-specific XML examples look at Bioassay XML examples for FTP section. No CSV files are permitted using FTP. You can also download templates of XML files from pending depositions that you are making in the Deposition Gateway. You will need one file with both the data and description filled out in the cases of new, data_only or replace_all operations. For the alter_descr operation, only the description should be filled out. Let's now reiterate these instructions by assay deposition operation:
XML Validation against PubChem XSD Schema To increase the efficiency of the data exchange for your Bioassay FTP submission, PubChem highly recommends that depositors first validate XML files before uploading them to the PubChem FTP site for processing. XML validation will make sure that your file conforms to the PubChem Bioassay specification and should help speedup the deposition time by isolating XML errors. To check if your XML document conforms to the PubChem XSD Schema, the XML document must be validated against that XSD Schema. You can find PubChem's XSD schema here. One XML validator that you might use is xmllint which is often included in standard Linux installations. To validate XML using xmllint one would run the following Linux command: xmllint --noout --schema "ftp://ftp.ncbi.nlm.nih.gov/pubchem/specifications/pubchem.xsd" FileName.xml Please be advised that PubChem does not support or maintain xmllint, but you can find more information on it here. Depositors may of course use any other equivalent XML package for validation. Assay FTP Deposition Communication and Processing As with substance FTP depositions, initial communication between you and our deposition system occurs through files in your FTP directory using a naming convention. Your input XML/ASN.1 file must end in ".in". Once that file is picked up by our system, it will try to process it and put the status of the deposition in another file with the extension ".status". There will also be a file ending in ".err" which will contain an explanation of any errors found. In some cases if a processing error occurs right at the start, the deposition will not have a status yet and the ".status" file will be empty. The status file informs you of the processing progress. The possible status file contents and their meaning are listed below.
After processing completes to the point of "Validated", you will need to log into the deposition system, review your submission, and then, if there are no issues, commit your data to be loaded into PubChem. An auto-commit feature can be requested, whereby the deposition commit step is performed on your behalf automatically. This removes the necessity for you to login and commit your data into PubChem. In many ways, FTP-based deposition is much like a normal deposited file. You can login to your deposition account at any time to see the progress of your deposition(s). Once you have resolved any processing errors that might come up, your assay will proceed to the validated stage. At this point, you can switch to the Deposition Gateway web interface and view your deposition. This gives you more interactive information about your deposition and is necessary for you to confirm the validity of your new assay or changes to your existing assay. From the validated stage you will no longer need the FTP system. 5. PubChem Deposition Documents and Examples Specifications
Examples
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