1. Publication content
What is an analyzed publication?
What is a captured publication?
What are the Aureus "key Journals"?
How are the other Journals (excluding “Key Journals”) entered into Knowledge bases?
Why can an article be missing?
Why is a patent missing?
Are review papers considered when building AurSCOPE knowledge bases?
What is the historical scope of Aureus knowledge?
2. Biological content
What type of biological information can be found in AurSCOPE knowledge bases?
Which target families are currently covered by AurSCOPE knowledge bases?
3. Chemical content
What type of chemical information can be found in AurSCOPE knowledge bases?
Does the molecular entry designation change as new names/synonyms are identified?
Are all the compounds from a patent registered?
4. Updates and releases
How often are knowledge bases updated, and what is the delay for a publication to be analyzed, captured, and available within AurSCOPE?
Are the publications "frozen" when they have been extracted in a release?
5. Quality
What happens when several publications report conflicting data for a given compound?
1. Publication content
What is an analyzed publication?
An analyzed publication is an article or a patent which is selected, according to “keywords” in the title or in the abstract, carefully read by a scientific analyst. Some of them in which no quantitative SAR can be captured are rejected and therefore are not in the final AurSCOPE knowledge base.
What is a captured publication?
A captured publication is an article or a patent for which SAR data activities have been integrated in the knowledge base with all related biological protocol details as well as chemical structures. The list of captured publications corresponding to a specific query can be retrieved in AurQUEST using the “get publication” button.
What are the Aureus "key Journals"?
The key journals are a set of journals for which Aureus provides comprehensive coverage, by regularly looking at all tables of content.
For the Target families knowledge bases, the key journals are:
• J. Med. Chem.
• Eur. J. Med. Chem.
• Bioorg. Med. Chem.
• Bioorg. Med. Chem. Lett.
For the ADME knowledge base the key journals and the period for full coverage are indicated below:
• Drug Metab Dispos 1997-2008
• J. Med. Chem 1998-2008
• Bioorg. Med. Chem. Lett. 1991-2008
• J Clin Pharmacol 1990-1997/2000-2008
• Br J Clin Pharmacol 1996-2008
• Clin Pharmacol Ther 2000-2008
• J. Pharmacol. Exp. Ther. 1999-2008
• Biol Pharm Bull 2001-2008
• Bioorg. Med. Chem. 1993-2008
• Xenobiotica 2000-2008
• Mol. Pharmacol. 1999-2008
• Life Sci (>1973) 2000-2008
• Eur J Clin Pharmacol 2000-2008
How are the other Journals (excluding “Key Journals”) entered into Knowledge bases?
The tables of content of principal pharmacological journals are screened to select important articles in which SAR data has been published. At this stage, a priority assessment based on ‘novelty’ and ‘added value’ is performed. Selected papers are analyzed and data is recorded by Aureus’ scientific analysts.
In addition, regular PubMed queries on ”hot” or new targets or on missing compounds are made to collect additional references of interest.
Currently, depending on the topic, we have between 100 and 360 different journals included in our current knowledge bases.
Why can an article be missing?
An article published in a “key journal” containing SAR data relevant to covered topics should be integrated in the Aureus platform. Nevertheless sometimes the article cannot be recorded or extracted in the release for a variety of reasons typically associated with data consistency or quality.
As Aureus would like to insure the maximum quality possible, we do not deliver data which we suspect to include an error. In this case the publication is re-reviewed to see if the suspected error can be corrected. However, if you believe we are missing a publication that should be in the database, please send us information on this to contact@aureus-sciences.com and we will rapidly get back to you on this matter.
The most common reasons why a publication is missing are the following:
• Document too recent to be included in the current release as the databases are quarterly updated.
• Quality control has detected an error and the paper has been blocked until a full review is completed.
• No quantitative SAR data available in the paper or the biological protocol is adequately described so the reference does not meet the Aureus criteria to be included.
• References were published in a journal not identified as a “key journal” or “additional key journals” and not appearing in our most recent Pubmed queries.
Aureus has developed a strict process for article selection and analysis, presented in the scheme below:
For a patent selected on “Targets Keywords”, only one patent per family is captured.
We do not capture Japanese patents; we wait until an English version is available.
Are review papers considered when building AurSCOPE knowledge bases?
Review papers are not captured in AurSCOPE Knowledge bases as we would like to avoid duplication of data. Aureus prefers to consider the original publication.
Nevertheless, review papers are used particularly to complete the bibliographical references indexed and finally access to additional original data points and eventually some additional compounds.
What is the historical scope of Aureus knowledge?
For the target knowledge bases, there is no limitation in term of time to select and record publications. The oldest publication integrated in AurSCOPE Knowledge bases is from 1940; however, we do concentrate on recent years to ensure full coverage of new data. For the ADME database 89 % of the content is from documents published after 1990.
2. Biological content
What type of biological information can be found in AurSCOPE knowledge bases?
Each quantitative result will be described in relation to the experimental context used by the authors and described in the publication. Both in vitro (Binding, Isolated organs, Enzymology…) and in vivo protocols are described in detail. Pharmacokinetics is included as part of the in vivo protocols.
Every detail of biological protocols is captured from the material and methods section of a paper and carefully organized using specific glossaries. A precise description of the biological material, the target and the experimental conditions is recorded and will be found within the corresponding AurSCOPE database.
Which target families are currently covered by AurSCOPE knowledge bases?
Currently Aureus Sciences has released target knowledge bases covering:
• GPCR
• Ion Channels
• Kinases
• Nuclear Receptors
• Proteases
Additional sets of data are available for Transporters, HSP90, Phosphatases.
3. Chemical content
What type of chemical information can be found in AurSCOPE knowledge bases?
• From a structural point of view; chemical structures with salt (and stoechiometry), radiolabel, stereochemistry, chiral flag, optical rotation are included. A unique Aureus ID is provided for each different compound (ID_MOL).
• Names fields for the molecule include: generic name and synonyms, pharmaceutical company codes. For a peptide, its sequence with any modification of any amino-acid is given.
• Therapeutic class.
• DrugBank status (Approved, Withdrawn, Experimental/Investigational)
• Molecular weight and classical physico-chemical descriptors (PSA, PKa, logP, logD, HBA, HBD…) (calculated values).
• For all structures, a Lipinski-Veber radar is presented in which in blue you see the characteristics of a molecule and in red the theoretical Lipinski-Veber limits.
Does the molecular entry designation change as new names/synonyms are identified?
Yes, any new information detected in publication for a molecule is verified and added.
Are all the compounds from a patent registered?
Following the patent analysis process (see above), all the molecules with non modulated quantitative activity point will be captured. For patents with activities expressed as ranges or modulated values, only a set of representative scaffolds will be registered.
The representative scaffolds are chosen by a medicinal chemist taking into account the ring size, number of rings or heteroatom in an effort to choose the most chemically diverse scaffolds.
4. Updates and releases
How often are knowledge bases updated, and what is the delay for a publication to be analyzed, captured, and available within AurSCOPE?
Every 3 months, a new knowledge base release is made available (March, June, September and December).
The delay for a publication from a key journal varies from one month to a maximum of 3 months.
For other journals, the delay depends on the way they are selected and prioritized. Any priority or specific request are welcome and should be addressed to your account manager or to contact@aureus-sciences.com.
For a patent, the delay to be analyzed and captured varies from one month to a maximum of 6 months depending on the patent provider and the complexity of the document -some patents contain a large amount of information or are complexly written; thus the careful analysis may be more time-consuming.
Are the publications "frozen" when they have been extracted in a release?
A publication is never “frozen”, at each release, new quality controls are run on the entire set of publications of a given project and data are corrected and updated. A full version of AurSCOPE knowledge bases is then delivered to our customer and available on the Aureus web portal AurWEB.
5. Quality
What happens when several publications report conflicting data for a given compound?
When several conflicting data points are published (i.e. in several different sources), all data points are recorded in the knowledgebase with the full detailed description of the experimental protocol used by the authors. This allows the end user to check for the most reliable data according to the experimental protocol details. In addition, if available, statistical elements, mean standard errors, standard deviations, number of experiments are recorded in order to give the clearest overview of the data consistency.
Statistical analyses for errors detection are also run on sets of publications by Aureus during our quality insurance process. We generate a report in the case when, for the same molecule tested in the same conditions (Target, Biological material…), an important delta between the data is observed (this is done when a minimum of 3 data points are collected with the same criteria).