Software & Application Release Notes

 

10/22/15 LSKB Version 5.0 Release Notes:

This document describes the functions that were added and the modifications that were made to version 5.0 of “LSKB – Life Science Knowledge Bank”. 

 

[Highlights]

  • Major upgrades to detailed information about diseases - in addition to listing a description, LSKB now provides variant information about related genes, and target proteins or chemicals associated with the disease in one page.

  • Generate various annotation tables by searching from a list of either gene IDs or protein IDs, and view it directly in LSKB’s browser.

  • "Predicted Affinity" is a value of a weighted average of an activity value and a similarity value. This value (score) is used for both "Target Prediction" and "Target Confirmation". Substructure search is part of Structure search, and "Target Confirmation" is also a target prediction function which lists all the compounds that have a common substrucure (the input)

 

 [New Functions・Modifications]

  • New Functions

The following single-function applications have been added to LSKB:

 

  • Variant Analysis Workflow

Using a VCF file as an input, this application runs SnpEff, then adds annotations to the variant analysis results from the LSKB DB and displays the a table format in the browser.

 

  • Expression Analysis Workflow

This application generates a list of gene expression annotations from LSKB DB for each row of an NGS data file.

 

  • Target Prioritization Analysis

This application generates a list of annotations using LSKB DB by inputting a list of gene IDs or protein IDs.

 

  • Compound Target Activity Matrix

From a list of gene or protein IDs, this application retrieves a list of assay data and related target proteins using curated data from ChEMBL.

 

  • PDB Activity Finder

From a list of PDB IDs, this application retrieves a list of assay data and related target proteins using curated data from ChEMBL.

 

  • Gene/Protein ID Table

This application displays a list of IDs that correspond with an input list of gene or protein IDs.

 

  • Target Prediction Batch

Drag and drop a chemical structure file in SD format or MDL MOL format, and this application generates a list of targets and analogical proteins from the entered compound by collecting assay information on similar compounds from ChEMBL data.

 

  • Assign Pharmacological Actions

This application produces a list of available chemical IDs from LSKB (LSKB ChemID) and the related pharmacological actions based on MeSH data.

 

  • Molecule-TTD/ICD10 Data Browser

This application shows a list of molecular structures and the related TTD/ICD10 information.

 

  • ChEBI Data Browser

  This application shows molecular structures and the corresponding information from ChEBI data.

 

  • Disease Detail

Search from a disease name, and LSKB provides a description, related genes, variant information, therapeutic target proteins, and chemical information in one page.

 

  • Structure Search

  • A “Target Confirmation” function was added for searching known targets using Substructure Search.

  • “Predicted Affinity” from the weighted average of activity and similarity values was added to be used as a score to calculate “Target Prediction” function.

  • The lower limit of similarity value has changed 50 to 40 in the query input screen.

  • The bug dealing with Stereo Chemistry as using GGA Ketcher in the query input has been fixed.

 

  • Data Management

  • Target (Gene or Protein)

    • The name of “Gene Group” has been changed to “Target (Gene or Protein)”

    • Multiple columns of gene IDs can be registered

    • UniProt ACC can be registered

  • Assay-Data

    • Cell Line ID, PMID, and Patent ID were added as registered column classes

  • ”Sub Species” tag was added as registrable General Info

  • Project filtering function was added in a PD tab in the SNP-Detail page

  • ”send To Variant Analyzer” function was added to execute variant analysis using SNPs data as an input

  • ”send To Expression Analyzer” function was added to execute analysis processes from expression analysis data as an input

  • ”Literature Matrix” function was added to see the number of co-current publications with genes in a TSV file, ratios, and p-values in a matrix format when the data is registered with one of Chemical / Disease / Tissue tags

  • Comment columns in TSV files can be saved, displayed, and exported

  • Info column data size in input data can be over 4,000 bytes

  • Drag & Drop operation is available for uploading TSV files

 

[User Interface]

  • Switching old and new interfaces is no longer available and all functions are compatible in the new interface

  • New “File” tab was added to the main menu. Even though uploading a file was a part of “Multiple Search” function, having the tab enables execution of expression statistical analysis, and the Expression Analyzer and Variant Analyzer applications

  • Updated Disease Detail, LSKB can list a description, related genes, variant information, therapeutic target proteins, or chemicals from a disease in one page

  • ”Quick Login” the previous version of LSKB required users to log back in using the external log-in page after the session timed out or became unavailable, now users can log back in from an open page

  • Four tree types: Protein Target, ATC Classification, Taxonomy, and MeSH Anatomy were added to “Tree Browser” in order to see a “Tree” based on each categorized item or purpose

  • Drag & Drop operation is available for uploading files to Multiple Search.

  • Reference information is available in a PDB detail page

 

[Additional Contents]

  • Data of Human dbSNP142 (GRCh37, GRCh38), SNP and disease Reference IDs from the dbSNP142, and a 3D viewer showing the mutation position in relation to the ligand were added

  • Data from NCBI MedGen and NLM UNLS was added into the LSKB disease dictionary

  • Mechanism data from ChEMBL was added

  • A mapped table, showing a mutual relationship to ATC Code and ICD10 was added

  • Therapeutic Target DB is now included

  • Compounds from UNII are now in LSKB

  • Compounds from BindingDB are now included

  • SureChEMBL in EBI ChEMBL was added

  • Text-mining data from dbSNP, targeting rsID, were also added

 

[System Matters]

N/A

 

04/22/2015: Metagenome@Kin ver. 2.2

1. Display a table of PCA rotation info

  • This tells which strains have strong affects on dispersion of sample arrangements according to PCA analysis

2. Retention of classifying bacteria names (optional)

  •  If different strains are classified with the same percentage of hits by BLAST, the classification will be pended at the rank and described as "Not determined" instead. 

3. Metagenomic analysis for fungus

  •  Using a RDP classifier executed result file, following functions are available: classification analysis from Genus rank by 16srRNA and classification analysis from Species rank by the ITS1/2 array

4. Ability to select which of 4 16S databases from which to execute Metagenome@KIN

  •  Users can select which 16s database (.mdb file) to use from a pull down menu

5. Reporting function - a report in HTML format will be exported, including all results from analysis (Fire Fox is required) 

 

08/18/2014: Metagenome@Kin Ver 2.0

New Features and Improvements:

  • Program now runs in Java­—Excel no longer required

  • Unlimited number of leads can be used for analysis

  • Enlarge a partial sunburst graph in any hierarchy

  • Clearer frequency analysis results, including the hierarchical structure by sunburst graph

  • Analyze the RDP classifier results file (Classifier.txt)

  • Execute cluster analysis and frequency analysis in a single operation

  • "Rejected" results (reads that did not pass through the BLAST filter) can be displayed in the graph

  • For users of World Fusion’s free local BLAST program, those results can now be included in the graph, such as the number of “no BLAST hit” reads (a lead that has not been assigned a bacterial name

 

LSKB Ver4.3.0 Release Note

04/01/2014: Product Update Release LSKB4.3 The compound search was made more useful by the classification of the protein contents into enzyme, GPCR, and KINASE.  Patent information on the compounds was added, enabling access to patent information via structure search.  The in-house experimental data management was also enhanced, with the ability to search & compare your own research data to the original LSKB knowledge bank including genes, chemicals and diseases. It was equipped with molecular framework as the backbone of the compound.

 

LSKB Ver4.2.0 Release Note

New Features:

  • Added dictionary based suggestion feature on each of the keyword search input fields

  • Added web based structure functions

  • Added molecular framework to all chemical structures

Updated and Discontinued:

  • Updated disease dictionary

  • No longer necessary to calculate activity values and ligand efficiency values - precalculated data now included in LSKB original data base

  • Updated ChEMBL database from ChEMBL Ver.13 to Ver.14

 

 

LSKB Ver4.1 Release Note

New Features:

  • Added activity value to the ChEMBL assay data

  • External program interface

  • Added cancel function for Batch search

  • Expanded UniProt and TrEMBL species

Updated and Discontinued: 

  • No longer supports creating a gene dictionary using GenBank entries

  • Add calculated pACT, BEI and SEI values to the LSKB annotation

 

If the selected records assay type belongs to IC50, EC50, Ki, Kd and the activity value is fixed, i.e. the relation is "=" and unit id nM, add calculated pACT, BSE, SEI into additional annotation.

 

pACT

pACT = - log10(IC50 * 10^-9) for IC50

BEI

BEI = pACT * 1000 / MW_freebase

SEI

SEI = pACT * 100 / PSA (Polar Surface Area)

DRUG DISCOVERY • TARGET PREDICTION • CHEMICAL GENOMICS • BIOINFORMATICS • VARIANT ANALYSIS • GENE EXPRESSION • GENOMIC RESEARCH

© 2017 World Fusion Co. Ltd. All rights reserved.