T09-2024 Release of BIOVIA Available Chemicals Directory 2024.02

Release of BIOVIA Available Chemicals Directory 2024.02

February 2024 (download file)

Release of BIOVIA Available Chemicals Directory 2024.02

Dear BIOVIA Available Chemicals Directory Customer,

Thank you for your continued use and support of BIOVIA products. We are pleased to announce that BIOVIA Available Chemicals Directory and its family of products are now available for download from the Dassault Systèmes Download Platform. Each download requires a separate license.

The Available Chemicals Directory family consists of BIOVIA Available Chemicals Directory (BIOVIA ACD), BIOVIA Chemical Products Information File (BIOVIA CPI), BIOVIA Available Chemicals Directory SDfile (BIOVIA ACD SDfile), and BIOVIA Available Chemicals Directory RDfile (BIOVIA ACD RDfile).

The database package includes a separate format for each of the following:

■         Direct 2020 format compatible with BIOVIA Direct 2020

■         Direct 2021 format compatible with BIOVIA Direct 2021 or 2021 SP1

■         Direct 2023 format compatible with BIOVIA Direct 2023

■         Data Mart format for BIOVIA Direct 2020

■         Data Mart format for BIOVIA Direct 2021 or 2021 SP1

■         Data Mart format for BIOVIA Direct 2023

BIOVIA provides support though the Dassault Systèmes global support site at https://www.3ds.com/support, where you can create and manage your service requests, explore the Knowledge Base and product documentation, join user communities, and access the Dassault Systèmes Download Platform. The support end date for each format is the same as the support end date of the corresponding BIOVIA Direct version. 

Notes:

■         Direct 2019 format databases are no longer available.

■         Direct 2020 and later formats apply a new representation for Haptic Bonds and use Self-Contained Sequence Representation (SCSR) for biological sequences.

■         Direct 2021 format was built with BIOVIA Direct 2021 SP1.

■         Direct 2022 and 2024 formats will not be released. For instructions on upgrading, see Chapter 6, ‘Upgrading Indexes’ in BIOVIA Direct Administration Guide.

■         Direct 2023 format is now available.

■         BIOVIA CISPro Customers: Your license includes the BIOVIA CISPro PCID and Firecode database to install with ACD Data Mart. Starting with ACD 2021.03, ACD Data Mart includes additional no-structure compounds (biological materials and supplies). For more information, see the Data Mart format section of this document.

784 supplier listings are described in the catalogs.pdf file that is included in the download package. The listed ACD suppliers have confirmed that most of the product listings are current. BIOVIA is committed to continuously improving the quality of the ACD database as well as updating its list of suppliers. The ACD Direct readme.txt includes the list of supplier codes that were added, deleted, or changed with this release.

If you would like BIOVIA to add additional chemical suppliers to the database or report any problematic suppliers, please follow the instructions in BIOVIA-How-to-List-Your-Products-in-BIOVIA-ACD-BIOVIA-SCD.pdf or email List_custom_BIOVIA_ACDSuppliers(at)3ds.com.

† 3D Models and CCRATIO (Close Contact Ratio) are generated with Pipeline Pilot protocols.

* BIOVIA removes suppliers from ACD if we are unable to verify their existence, if the products listed are no longer offered, or if requested by the supplier. Chemicals that are not listed in any current supplier catalog are also removed. If the chemicals reappear in future supplier catalogs, they are re-added, flagged as “New in ACD,” and identified by re-using the MDL numbers that the chemicals had previously used. The mdldiff.txt lists changes. For more information, refer to the readme.txt.

** Add 2 GB to the ACD Data Mart schema, if you import CISPro Contents (PCID and FireDB) database tables.

Notes:

■         Tablespace size varies between Oracle instances. Expect variance from the values reported in the table above, in tbl_inddirect.lst, or tbl_ind.lst. The storage requirements refer to used space after the databases are installed. Direct formats may require up to 25% additional tablespace during the import process to create the domain indexes. Ensure that the tablespace is large enough or set autoextend “on”.

■         As of the ACD 2017.10 release, 3D structures are produced using a BIOVIA Pipeline Pilot protocol to align with other BIOVIA software products. CORINA^© is no longer used.

■         CAS Registry Numbers (RN) were not verified by CAS and may be inaccurate. If a chemical has multiple CAS RNs, the most commonly used RN is typically applied.

You can install ACD Direct and Data Mart formats within the limits of your current license.

BIOVIA ACD – Direct format

Direct format of BIOVIA databases require a database server platform with an Oracle Database and BIOVIA Direct installed. According to the Dassault Systèmes’ Platform Support Policy, Oracle is the third party software, and that follows the third party vendor maintenance and support policy (including, but not limited to, the lifecycle policy of the third party vendor). Oracle tablespace requirements are listed in the first page of this document. The Oracle information and requirements for Direct are included in the BIOVIA Direct System Requirements Guide in your version of BIOVIA Direct Documentation package.

When importing BIOVIA commercial databases into Oracle instances that do not use the AL32UTF8 character set, you might see a warning and the database import log file might include these lines: “possible data loss in character set conversions.” You can ignore this warning message because there is no data loss.

Globally Harmonized System of Classification and Labeling of Chemicals (GHS) has been added in the ACD2D_PRODUCT_DATA table. To display the GHS data, use the SQL select command including "PROP_ID=3 and VALUE_CHAR like 'GHS %'". For more information, see the ACD Direct readme.txt.

Starting with ACD 2021.11, ACD2D_OHSLINK table will no longer include the data, because UL (formerly ChemAdvisor) will discontinue the “EH&S Data Elements” that provided the OHS Numbers to access to their MSDS Websites for some applications.

Starting with ACD 2019.08, the format of MDLDIFF.TXT has changed to accommodate Catalog Numbers that contain more than 12 characters. For more information, see the ACD Direct readme.txt.

Starting with ACD 2016.11, CAS numbers are uniquely associated with MDL numbers. Therefore, ACD2D_CAS.CASFLAG no longer includes ‘X’ flag. The ‘P’ flag is kept to maintain compatibility with searches that still look for this value.

Notes:

■         BIOVIA Insight customers can download and install the IDS files and query/browse forms to search with Insight. Please visit the Dassault Systèmes BIOVIA Download Platform at https://software.3ds.com (requires login), select Release: 2024 and Level: BIOVIA 2024 Golden. Then go to BIOVIA Insight download area and download BIOVIA_2024.DB_Insight_IDS_forms.zip. Instruction is available in the Technical Note T27-2019 “BIOVIA Database IDS and Forms for Insight”.  Insight IDS and Forms are supported with Insight 2017 and later.

■         The default Isentris IDS files and Isentris Client forms may not display 3D structure, because the default IDS files are configured for use with Direct 8 and earlier. You must install Isentris 4.0 SP3 or later and modify the ACD_IDS.xml as instructed in the commented lines in the ACD_IDS.xml. For more information, see the BIOVIA Isentris Administration Guide.

BIOVIA ACD – Data Mart format

Direct format of BIOVIA databases require a database server platform with an Oracle Database and BIOVIA Direct installed. According to the Dassault Systèmes’ Platform Support Policy, Oracle is the third party software, and that follows the third party vendor maintenance and support policy (including, but not limited to, the lifecycle policy of the third party vendor). Oracle tablespace requirements are listed in the first page of this document. The Oracle information and requirements for Direct are included in the BIOVIA Direct System Requirements Guide in your version of BIOVIA Direct Documentation package.

IMPORTANT:

■         Starting with 2021.03, ACD Data Mart has additional records of no-structure biological materials or lab supplies from chemical supplier catalogs. Those records are included in the ACD Data Mart only, and to use with CISPro for importing Biological or Supply from the ACD Data Mart. MDLNumbers are not assigned to them.  

ACD Data Mart stores all available products and package information from the corresponding ACD database, for use with BIOVIA CISPro.

■         Starting with BIOVIA CISPro 2018, the only requirement for ACD searches is ACD Data Mart.

■         With BIOVIA CISPro 2017 R2 SP2 and earlier releases, ACD search requires an ACD database.

For more information, see BIOVIA ACD Data Mart Installation Guide (biovia_acd_datamart_inst_v1.pdf), which is included in the download package. For information about Oracle table updates, see the ACD Data Mart readme.txt and BIOVIA_acddatamart_book_v1.pdf that has the ACD Data Mart table descriptions. 

If you enable the CISPro PCID Sync (Pure Compounds Inventory Database), the Fire Code and FireDB Sync modules, you must import the BIOVIA CISPro PCID and Firecode database dump file extchemdata2020.dmp into the ACD Data Mart schema. The BIOVIA CISPro PCID and Firecode database is available on the Dassault Systèmes Download Platform by selecting:

Release: BIOVIA Content 2024

Level: BIOVIA Content 2024 Golden

And find BIOVIA CISPro PCID and Firecode.

For more information, see the BIOVIA CISPRO Content 2020 Installation Guide (BIOVIA_CISPro_Content_2020_InstallationGuide.pdf), which is included in the download package.

Space requirements for CISPro Content database:

■         Add 2 GB to the ACD Data Mart schema

BIOVIA CPI

The BIOVIA Chemical Products Information File (BIOVIA CPI) requires a database server platform with an Oracle Database installed. According to the Dassault Systèmes’ Platform Support Policy, Oracle is third-party software that follows the third-party vendor maintenance and support policy (including, but not limited to, the lifecycle policy of the third-party vendor).

Oracle Tablespace requirements:

■         CPI Server: Oracle tablespace 102 GB  (51 GB dump file size)

■         NSEARCH: Oracle tablespace 187 GB (89 GB text file size)

BIOVIA CPI is an Oracle relational database that has a matching collection of chemical catalogs from BIOVIA ACD, without chemical structures. This release of BIOVIA CPI includes CPI Server and NAMESEARCH index.

Notes:

■         Starting with CPI 2019.05, CH_CASRN column in the CHEMICAL table matches with the primary CAS number flagged as ACD2D_CAS.CASFLAG='P' in the ACD Direct format database, if there are multiple CAS numbers associated to a chemical in ACD.   

■         Starting with CPI 2019.04, PI_STRING column in PERMUTED_INDEX table has changed from datatype CHAR(5) to VARCHAR2(10) to accommodate multi-byte characters that are included in chemical names.

■         Globally Harmonized System of Classification and Labeling of Chemicals (GHS) was added to the PRODUCT.PRD_DESC and DESCRIPTION.DS_TEXT fields.

■         For the entity-relationship diagram, see cpi_book.pdf.

BIOVIA ACD SDfile

BIOVIA ACD SDfile contains 2D structures and 3D models (see note) for 15.7 million unique chemicals and associated structure data; they do not contain supplier data. This product can be used by itself or in conjunction with BIOVIA ACD RDfile. The file BIOVIA_CTFileFormats.pdf is included. This file describes the connection tables used in the SDfiles to specify the chemical structures and models.

Space requirements:

■         2D SDfiles total: 18 GB, 3D SDfiles total: 30 GB

Note: Starting with ACD 2017.10, 3D model structures and Close Contact Ration (CCRATIO) are generated with Pipeline Pilot protocols.

BIOVIA ACD RDfile

BIOVIA ACD RDfile provides supplier related information for 48.6 million products selected from 784 catalogs and 2D structures. It does not contain models and associated 3D data. The file BIOVIA_CTFileFormats.pdf is included. This file describes the connection tables used in the RDfiles to specify the chemical structures.

As of the ACD 2019.01 release, BIOVIA ACD introduced a new RDFile format. The previous RDfile format included limitations inherited from ISIS, which is no longer supported. These limitations included:

■         Catalog numbers limited to 12 characters

■         Strings greater than 80 characters broken into more than one line

■         Supplier data limited to 9999 lines

■         Lacked additional property data such as density, numeric density, boiling point, refractive index, and so on

These limitations are removed in the release of the new RDfile format.

Changes in the New Format

■         Strings whose length exceeds 80 characters are no longer broken into separate 80-character lines separated by a plus sign (+).

■         In the SUPPLIER field, the lines containing package information have changed.

¡  ‘_F’ and ‘_B’, which were often arbitrarily assigned, are replaced with ‘_P’.

¡  The catalog number is presented as it appears in the database, followed by a space.

¡  The catalog number is no longer limited to 12 characters.

■         The SUPPLIER field can be of any length and overflow MDL numbers are no longer used. Previously, RDfiles were limited to 9999 lines and additional data was continued to one or more overflow MDL numbers.

■         Values for the SUPPLIER.INDEX field are now two space-delimited integers instead of consecutive four-character fields.

For details about the formatting, refer to the readme.txt in the RDFile format download package.

Space requirements for RDfiles:

■         61 GB of free space

Getting Help

Visit the Support site at https://www.3ds.com/support/, where you can:

■         Call us

■         Submit a request

■         Access downloads

■         View hardware and software requirements

■         Visit the knowledge base

Sincerely,

Chemical Sourcing Database Production Team

Dassault Systèmes BIOVIA