Autoregistration
The Registration page (also known as the autoregistration page) is the second page of the web client application, from where a compound can be sent for registration.
This chapter gives you a walkthrough of the usage of the Registration page:
Structure area
In order to draw a structure, just simply click on the str ucture area and th e structure editor will load ( figure Autoreg 1 ) . The default structur e editor is Marvin for JavaScript. For draw in g structures, optionally you can also use Marvin applet or ChemDraw. To see how the structure editor can be chan ged please con sult the user Profile page.
Figure Autoreg 1. The Registration page
After loading or drawing a structure the user has the possibility to "quit" the editing of a structure: just simply click the [Save & close] button located at the upper left side of the editor. By closing the structure editing mode, other functionalities will be available:
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Structure type can be changed
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Salt/solvates can be added
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Chemically Significant Text (CST) can be added
Structure type can be: Single, Mixture, Formulation or Alternate. Here instead of a single structure, multi-component compounds can be set in order to be registered.
Salt/solvates can be added from a Salt/solvate list, where previously salts and/or solvates were uploaded or added.
CST, if exists, can be attached to the chemical structure (considered part of the structure), and takes part in defining the structure uniqueness. CSTs, previously added to a dictionary (see Administration page, Dictionary manager tab), can be retrieved during autoregistration (and also during manual registration and amendment) from a drop-down list .
Compounds with no structure
It is possible to register compounds having no structure, just CSTs. These are not autoregistered, unless the CST is present in a Dictionary, but they can be successfully registered from the Staging area. Compounds with only CSTs (no structure) will have a star atom in the structure area.
Depending on the appropriate settings (registration source; structure validation; CST; Submitter ID; external ID like LnbRef, lot ID; etc.) for a given compound, the registration can be performed automatically (autoregistration), or the submission ends up in the Staging area.
Validation, Standardizing and Structure Checking/Fixing
Before registering a structure and/or CST, the compound is first validated, standardized, checked and fixed. After this process a match search is performed.
Additional parameters can also be the PCN and CN fields, in which specific IDs can be set for the compounds to be registered.
Validation
The following validation steps are performed during the autoregistration process:
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User ID validation (at login)
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Source validation
If the source validation is on, but the given source doesn't exist in the DB, the submission will fall to the Staging area, from where it will be possible to register it, even without being able to change it.
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External ID (e.g. LnbRef, Lot ID) validation (check for the uniqueness of the IDs):
The format of the LnbRef can be customized (see Validation Rules) and it is validated during the registration process. A valid LnbRef format can be e.g. A12345 (a one character string followed by 2-11 digit number) but any other format is accepted if it can be described by a set of regular expressions.
The LnbRef can be modified after the registration, but the attached Lot ID cannot.
A valid Lot ID can be any positive integer number with a maximum of approximately 2×10^10. Zero, empty field or numbers followed by text are not considered valid Lot IDs, and therefore cannot be accepted. In these cases warning messages are displayed in red below the fields, like: "Please enter a positive value." If the registration process is started in spite of the first warning message, another message will be received:
Depending on how the "Reject id duplication" system switch is configured (for each source), the submission is either rejected (and therefore will not be present in the Staging area) or it will fall to the Staging area with "LnbRefDuplicated" or "LotIdDuplicated" status messages.
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The scale of salt and solvate multiplicity
Currently the default settings are 0 for the salt and 1 for the solvate multiplicity scale.
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The check for a positive charge
Structures having a positive charge cannot be registered, they will fall to the Staging area for more attention. For more details check the Submission correction page.
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The check for a balanced charge
Unbalanced structures cannot be registered, they will fall to the Staging area to be corrected. For more details check the Submission correction page.
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The check for the maximum number of components in case of mixtures
For the maximum allowed components a number can be set in case of mixtures. If this number is exceeded, the compound to be registered will fall to the Staging area to be corrected.
Further validation options can be configured using the source dependent system switchers. For more informations about the system switchers, please consult the Compound Registration Configuration Guide Validation Rules. E.g. when a given source is used, and the structure is not passing the check, the submission can be either:
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autofixed and autoregistered
e.g. chiral molecules with absolute configuration will be registered with an attached "Absolute" flag.
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or sent to the Staging area with different types of "StructureCheckerError". These submissions can be fixed on the Submission correction page by selecting the appropriate fixer from the list.
e.g. when trying to register a structure having a crossed double bond using source "ELNB", it will fall to Staging.
Then on the Submission page, the "convert to single bond" fix can be selected before the manual registering it.
Standardization
During the autoregistration the compound is standardized according to the following rules:
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Structure to be registered |
Registered structure |
Abbreviated groups will be expandedWhen drawing structures you can use abbreviations (e.g. ACE, COOEt, TBS, TBSO etc.). These groups will be automatically expanded on Submission page or Amendment page. It is possible to specify a list of exception abbreviations (e.g. Ala, Boc) that will be not expanded automatically |
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Aromatic structures are dearomatizedAromatic structures are converted to structures with alternating single and double bonds. E.g. when registering naphthalen-1-amine (left, aromatic form) it will be registered as non-aromatic |
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Charged nitro (or nitroso) groups are converted to groups with double bonds |
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Non-specific explicit Hydrogens are removed |
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Structure checking and fixing
After the validation and standardization, the compound undergoes structure checker steps, and some of the issues are fixed automatically. The structure checking is performed for both single compounds and multi-component compounds. The structure checkers and fixers are applied for all the submissions as 'Quality checks' (if the corresponding system switcher is set to true). Using Structure Checker a set of checkers can be choosen to be applied here during the registration process, or either custom structure checkers can be defined.
Example for structure checkers:
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Three Dimension Checker:
Thecker searches for 3D (Z) coordinates. Fixer offers: cleaning the structures by 2D clean and setting the atomic z-coordinates to zero. -
Rare element checker:
The checker searches for rare elements in the structures: atoms generally not present in organic compounds (E.g. Ru). No fix is available for this checker. -
Valence error checker:
Checker searches for valence errors. Fixer offers removing explicit hydrogens if applicable
If the checker is on, and the structure to be registered is not passing the quality check, the submission can be:
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either autoregistered (in case if the checker has an autofix)
e.g. structures containing radicals are automatically registered without any radical
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or not autoregistered, and sent to the Staging area for revision.
e.g. dicyclohexylruthenium will fall to the Staging area with "Registration failed" message because of the rare element checker defined within the quality checks. In order to register it, the Perform Quality Checks Switcher (from Staging, Submission page) should be turned off
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Perform Match search
After the validation process, the structure to be registered is checked for any exact parent matches (considering also CSTs). If the record has no structure and no CST, it cannot be autoregistered.
Autoregister a unique structure (no match)
If there is no parent exact match, the record will be registered as unique and a new tree is generated. New registration IDs (PCN, CN and LN) are generated by the system according to predefined rules, unless specific Ids (PCN and/or CN) are provided.
Registering a single compound
In order to register a single compound molecule, e.g. paracetamol, you need to set a valid, unique LnbRef (and, if needed, a unique lot ID), then click in the structure area: the Structure Editor will load and you can draw/import/paste the paracetamol's structure. (figure Autoreg 2).
On the Registration page, the default source is Registrar, the default Submitter is the logged in user, the default structure type is single structure. To register a compound just click on the [Register] button.
Figure Autoreg 2. Registration page when drawing a single type structure
After registering a unique compound, you'll be informed about the generated new PCN, CN and LN (e.g. PCN: CXN1, CN: CXN1A, LN: CXN1-001). The user will be offered to navigate immediately to the registered structure on the Details page.
Optionally, another button can be present, which - using an ID parameter (e.g. LnbRef) - can redirect the user to a specified URL (configurable).
Registering a multi-component compound
In order to register a multi-component compound (e.g. a mixture), follow the next steps:
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Click on the structure editor and draw the first component. The default range for the first component is 21-44%. If you finished editing the first component, click on the [Save & close] button.
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Set the structure type to mixture (alternate or formulation).
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Click on the plus sign.
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Click on the structure editor and draw the second component. The default range for the first component is 21-44%, change it, if you need it. If you finished editing, click on the [Save & close] button ( figure Autoreg 3 ).
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To add more components, repeat steps 1-3. If you've reached the desired number of components then click on [Register].
Figure Autoreg 3. Registration page when drawing a mixture component (Edit Mode)
There are 5 modes in the structure area: Edit Mode, Image View, List View, Grid View and Fullscreen.
Edit Mode
In the Edit Mode, beside adding or drawing structures, component CSTs and ranges (Mixtures) / percentages (Formulations) can be added.
It is possible to navigate between components by the aid of navigation arrows: Component 1, Component 2, Component 3, 3 Components ( figure Autoreg 3 ).
When all components are present, the add salt/solvate functionality and the CST box for the multi-component compound will be available too (figure Autoreg 4).
In Edit Mode the [Load from database] option ( figure Autoreg 3 ) is also available. When clicking on it the [Load component by PCN] window will open, where a PCN can be entered. Using this option is possible to load a structure (considering also CSTs, but no additional data) from an already registered parent compound, to be again registered, possibly as a new lot in an existing tree, or, to be further modified before registration.
Figure Autoreg 4. Registration page when editing a 3 components mixture (Edit Mode)
Image View
In Image View all functionalities of the components and compounds, available in Edit Mode, will disappear. In the structure area the fused image of the compound will be available.
List View
In List View all components are listed without their structure, but component Ids and component CSTs, if available, and the ranges of mixtures (figure Autoreg 5) are present. In List View components can be deleted or loaded from the registry database if PCN is given (figure Autoreg 6).
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List View of the components in the structure area |
Load component by PCN |
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Grid View
In Grid View component structures with their component Ids and component CSTs, if available, and the ranges are aligned in a resizable panel (figure Autoreg 7).
Figure Autoreg 7. The grid view of the components in the structure area.
If the editing of the components is finished just simply click on the [Register] button. After the successful registration you can click on the [View Details] button and inspect the result on the Amendment page, where by default the lot level fused image is shownIf you click in the structure area, the first component will appear in the structure editor, then navigating with the arrows the other components can be accessed.
It is possible to autoregister a multi-component compound consisting of components with CSTs: e.g. set the structure type to alternate, draw octahydro-2-benzothiophene and set "comp1" in the component CST field of the first component, click on Add, then draw octahydro-2-benzofuran and set "comp2" in the component CST field of the second component, then click on Register. You can check the result on Amendment page. In case of the alternate structure type (having no information about the composition of the components) an unknown attached data "ALTERNATE 1" will be also added to the fused image (figure Autoreg 8).
Figure Autoreg 8. The generated fused image of a two component alternate with component CSTs (displayed on lot level) on View Details page.
Autoregister exact matches
Exact matches are automatically registered under the existing parent. All these cases require that the "RegisterNewLots" and "RegisterNewVersions" system switchers are set TRUE for the used source. Exact parent matches can be registered under an existing version in which case specified PCN and CN is not considered, or it can be registered under a new version with a specified CN (if there is one).
E.g. when registering 2-{2-[(2,6-dichlorophenyl)amino]phenyl}acetate with 1xNa+ as salt, and diclofenac is already present in the DB, a new version will be created and the preparation (lot) will be moved under it ( figure Autoreg 9 ).
Figure Autoreg 9. Tree with two versions
Register with CN option
It is possible to register a new lot under a given version (CN) without supplying the structure and/or CST and optionally salts/solvates. In order to do this, only external IDs (LnbRef, lot ID, if needed) and source fields have to be supplied, then the [Register with CN] button should be clicked and in the appearing Registering structure window the desired compound number (CN) should be entered. Next to the mandatory fields, additional data (e.g. Purity, QC, Project etc.) can also be supplied, which will be saved as lot level additional data. The Project name, supplied for the lot, will be inherited by the version and the parent too. Stereochemistry and Geometric isomerism data are not stored.
Autoregister non-exact matches
In case of a parent match that is not exact (e.g. 2D and/or tautomer), the submission will fall into the staging area or it will be successfully autoregistered depending on the actual system switchers of the source (if it is enabled to register 2D/tautomer matches or not).
System switchers include: "Register New Lots", "Register New Versions", "Register 2D Parent Matches", "Register Tautomer Parent Matches", "Register 2D-Tautomer Parent Matches", and "Register if matches are restricted". There are three more switchers with slightly different purpose, that can be configured in a source dependent way: "Analyze Salt Solvate Fragments", "Perform Quality Checks" and "Reject id duplication".
Independently from the match action (accept/replace parent matches), the compound to be registered can go under an existing version (in which case specified PCN and/or CN are not considered), or it can be registered under a new version (in which case specified CN, if there is one, is kept).
Autoregistering 2D matches
Autoregistering 2D matches can be allowed if the "Register 2D Parent Matches" system switcher is set TRUE for the used source. In this case the record will be registered under a new PCN and CN.
Autoregistering tautomer matches
Autoregisteing tautomer matches can be allowed if the "Register Tautomer Parent Matches" system switcher is set TRUE for the used source. In this case the record will be registered under a new PCN and CN. If the system switcher is set FALSE, the submission will fall to the Staging area with "ParentTautomeMatch" status message.
Autoregistering 2D&tautomer matches
Autoregisteing 2D&tautomer matches can be allowed if the "Register 2D&Tautomer Parent Matches" system switcher is set TRUE for the used source. In this case the record will be registered under a new PCN and CN.
Autoregistering new compounds with restricted matches
After a match is found for a newly registered compound it is also checked if the match is restricted or not. In case of a restricted match the submission falls to the Staging area with "RestrictedMatch" status message (if the "Register if matches are restricted" system switcher is set FALSE for the used Source). If none of the matches are restricted the record will be registered as a new lot either under an existing version (in case of a matching version), under a new version (if the version doesn't exist, but there is a parent exact match) or under a new parent (if it is a 2D/tautomer match).