From QSPR Wiki
1. Before data upload
Verify that the property you would like to introduce exists in the Properties Browser. It may appear that your property can have different name that you expect. Filter properties by keywords and search your property. If the property does not exist, create it. Decide whether it is qualitative or quantitative. In the former case introduce possible qualitative options (e.g., "active", "inactive") and in the later case decide which System of Units does it need. Select default Unit value for Properties. Some Properties may require Obligatory conditions, i.e. conditions that should be always indicated (e.g., "pH" for octanol/water distribution coefficient logD, Species for LD50, etc.). The obligatory conditions should be specified when a property is created. If Condition does not exist, create and add it in a similar way as a property.
N.B.! Before creating any new Property/Condition, please, verify whether it already exists. Currently it is impossible to modify existing properties/conditions. Thus, please, carefully design your property.
2. Upload data
Please introduce data in the original unit as found in the literature. Check, whether this unit already exists and create it with the conversation formulas from and to default unit, if necessary.
Make sure that the name of the article as in the literature is introduced into the Database, for otherwise data verification becomes really time consuming.
The easiest way to upload data is to use Batch upload browser using Excel or sdf file. The detailed instructions on how to do it and example of batch file are provided elsewhere. The most important things are as following.
- The source of data (article, report, book, chapter) should be provided in ARTICLEID field. If data are from article in PubMed, just use PMID there. If not, create the corresponding sources before uploading the data and use their QID numbers.N.B.! Name of molecule (or SMILES), Property and ARTICLEID is the minimal number of columns that is required to upload data.
- Indicate whether uploaded data were measured in the article (1 in REFERENCE field) or whether the given article is just a collection of data from other sources (leave REFERENCE empty or provide a QID to article with reference to the data, if such information is available).
- Upload data, remap columns if required, change default units to the actual ones and check errors if required.
- In general, carefully read instructions on how to prepare Excel file to avoid possible.
3. Verify uploaded data
The provided names of molecules will be checked against PubChem, i.e. for each name we will retrieve a structure from PubChem, which is considered as an Oracle. The name will be colored according following rules
- black - not yet checked
- green - uploaded structure matches PubChem molecule
- brown - uploaded and molecule in PubChem have different stereochemistry
- red - uploaded and stucture in PubChem for this molecule do not match.
Notice, that only first match (i.e., first structure retrieved from PubChem) is considered for comparison. If retrieved structure in PubChem does not correspond to the correct structure, the user can manually verify name by clicking [v] after the name. His/her pseudoname will be indicated as confirmation.
N.B.! The name of user who uploaded record ("introducer") and name of last user who modified it ("modifier") are shown as well as time when the change was done. If data were uploaded by a non-registered user, a first user who will edit them will become the "introducer".
4. Delete data
The user can delete records by selecting a set of records or one by one. The deleted data are not deleted immediately, but instead are placed in "trash" of the "introducer", who may decide to delete or restore them. The "introducer" will see who deleted the records.
N.B.! In order to avoid possible problems, when you delete data for which are not the introducer, send a message to the introducer and explain why do you want to delete these particular data. In case of conflict, contact administrator.
5. Hierarchy of users
The database support hierarchy of users. The system was developed to prevent intentional and unintentional damage of data by some users. Currently we have
- Guest or anonymous users
- Non-validated registered users
- Validated registered users
- Superuser (only one, "admin")
The lower rank users cannot modify/delete records of the higher ranks users. However, they can always send an e-mail using embedded mail-system to the higher level users and request them to make modifications. The role of "admin" is to take final decision in conflict situation and prevent further modification of data. The registered users will become validated following explicit request to the "admin" and/or following observation of a "correct" behavior of a user. Validated users can batch export any data stored in the database, while non-validated users can do it only for data introduced by them.