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LipidHome: a database of theoretical lipids optimized for high throughput mass spectrometry lipidomics.

Foster JM, Moreno P, Fabregat A, Hermjakob H, Steinbeck C, Apweiler R, Wakelam MJ, Vizcaíno JA - PLoS ONE (2013)

Bottom Line: While having a seasoned community of wet lab scientists, lipidomics lies significantly behind proteomics in the adoption of data standards and other core bioinformatics concepts.This work aims to reduce the gap by developing an equivalent resource to UniProt called 'LipidHome', providing theoretically generated lipid molecules and useful metadata.The web application encompasses a browser for viewing lipid records and a 'tools' section where an MS1 search engine is currently implemented.

View Article: PubMed Central - PubMed

Affiliation: EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom. jfoster@ebi.ac.uk

ABSTRACT
Protein sequence databases are the pillar upon which modern proteomics is supported, representing a stable reference space of predicted and validated proteins. One example of such resources is UniProt, enriched with both expertly curated and automatic annotations. Taken largely for granted, similar mature resources such as UniProt are not available yet in some other "omics" fields, lipidomics being one of them. While having a seasoned community of wet lab scientists, lipidomics lies significantly behind proteomics in the adoption of data standards and other core bioinformatics concepts. This work aims to reduce the gap by developing an equivalent resource to UniProt called 'LipidHome', providing theoretically generated lipid molecules and useful metadata. Using the 'FASTLipid' Java library, a database was populated with theoretical lipids, generated from a set of community agreed upon chemical bounds. In parallel, a web application was developed to present the information and provide computational access via a web service. Designed specifically to accommodate high throughput mass spectrometry based approaches, lipids are organised into a hierarchy that reflects the variety in the structural resolution of lipid identifications. Additionally, cross-references to other lipid related resources and papers that cite specific lipids were used to annotate lipid records. The web application encompasses a browser for viewing lipid records and a 'tools' section where an MS1 search engine is currently implemented. LipidHome can be accessed at http://www.ebi.ac.uk/apweiler-srv/lipidhome.

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Screenshot of the LipidHome “Browser” view.The LipidHome structural hierarchy can be navigated in the far left tree panel. Clicking on a lipid record produces two vertically stacked panels in the right hand panel. The top panel shows general information about the selected record including an image. The bottom panel displays a table of the selected records’ children lipids, i.e. selecting the “Sub Class” “Diacylglycerophosphocholines” provides a list of its “Species”. These lists are exportable to a number of file formats.
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pone-0061951-g003: Screenshot of the LipidHome “Browser” view.The LipidHome structural hierarchy can be navigated in the far left tree panel. Clicking on a lipid record produces two vertically stacked panels in the right hand panel. The top panel shows general information about the selected record including an image. The bottom panel displays a table of the selected records’ children lipids, i.e. selecting the “Sub Class” “Diacylglycerophosphocholines” provides a list of its “Species”. These lists are exportable to a number of file formats.

Mentions: The LipidHome web application is split into three main sections; “Browser”, “Tools” and “Documentation”. The “Browser” (Figure 3) is the core of the application where lipid records are navigated to and displayed. The interface is organised into two main panels. The left panel shows the lipid hierarchy tree: users can click the elements in this tree and they will be loaded into the right panel. Lipid records loaded into the right panel display information specific to the selected lipid in the top sub panel and a list of the record’s children in the bottom sub panel. For example selecting the “Sub Class” diacylglycerophosphocholines, will display an image and information about the “Sub Class” at the top and a list of its “Species” at the bottom. Records in the list can be selected to drill deeper down the structural identification hierarchy. Due to the large number of theoretical lipids stored in the LipidHome database, children of a selected lipid record (displayed in the table below the general information) are filterable by the table’s columns. As an example, the unidentified lipid records may be filtered out of the table by selecting the drop down menu of the “Identified” column header, hovering the mouse over “Filters” and selecting “Yes”. Alongside general information, cross-references and papers are available for some records (Figure S5 in File S1). From here links can be followed through to external resources with lipid specific information.


LipidHome: a database of theoretical lipids optimized for high throughput mass spectrometry lipidomics.

Foster JM, Moreno P, Fabregat A, Hermjakob H, Steinbeck C, Apweiler R, Wakelam MJ, Vizcaíno JA - PLoS ONE (2013)

Screenshot of the LipidHome “Browser” view.The LipidHome structural hierarchy can be navigated in the far left tree panel. Clicking on a lipid record produces two vertically stacked panels in the right hand panel. The top panel shows general information about the selected record including an image. The bottom panel displays a table of the selected records’ children lipids, i.e. selecting the “Sub Class” “Diacylglycerophosphocholines” provides a list of its “Species”. These lists are exportable to a number of file formats.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3646891&req=5

pone-0061951-g003: Screenshot of the LipidHome “Browser” view.The LipidHome structural hierarchy can be navigated in the far left tree panel. Clicking on a lipid record produces two vertically stacked panels in the right hand panel. The top panel shows general information about the selected record including an image. The bottom panel displays a table of the selected records’ children lipids, i.e. selecting the “Sub Class” “Diacylglycerophosphocholines” provides a list of its “Species”. These lists are exportable to a number of file formats.
Mentions: The LipidHome web application is split into three main sections; “Browser”, “Tools” and “Documentation”. The “Browser” (Figure 3) is the core of the application where lipid records are navigated to and displayed. The interface is organised into two main panels. The left panel shows the lipid hierarchy tree: users can click the elements in this tree and they will be loaded into the right panel. Lipid records loaded into the right panel display information specific to the selected lipid in the top sub panel and a list of the record’s children in the bottom sub panel. For example selecting the “Sub Class” diacylglycerophosphocholines, will display an image and information about the “Sub Class” at the top and a list of its “Species” at the bottom. Records in the list can be selected to drill deeper down the structural identification hierarchy. Due to the large number of theoretical lipids stored in the LipidHome database, children of a selected lipid record (displayed in the table below the general information) are filterable by the table’s columns. As an example, the unidentified lipid records may be filtered out of the table by selecting the drop down menu of the “Identified” column header, hovering the mouse over “Filters” and selecting “Yes”. Alongside general information, cross-references and papers are available for some records (Figure S5 in File S1). From here links can be followed through to external resources with lipid specific information.

Bottom Line: While having a seasoned community of wet lab scientists, lipidomics lies significantly behind proteomics in the adoption of data standards and other core bioinformatics concepts.This work aims to reduce the gap by developing an equivalent resource to UniProt called 'LipidHome', providing theoretically generated lipid molecules and useful metadata.The web application encompasses a browser for viewing lipid records and a 'tools' section where an MS1 search engine is currently implemented.

View Article: PubMed Central - PubMed

Affiliation: EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom. jfoster@ebi.ac.uk

ABSTRACT
Protein sequence databases are the pillar upon which modern proteomics is supported, representing a stable reference space of predicted and validated proteins. One example of such resources is UniProt, enriched with both expertly curated and automatic annotations. Taken largely for granted, similar mature resources such as UniProt are not available yet in some other "omics" fields, lipidomics being one of them. While having a seasoned community of wet lab scientists, lipidomics lies significantly behind proteomics in the adoption of data standards and other core bioinformatics concepts. This work aims to reduce the gap by developing an equivalent resource to UniProt called 'LipidHome', providing theoretically generated lipid molecules and useful metadata. Using the 'FASTLipid' Java library, a database was populated with theoretical lipids, generated from a set of community agreed upon chemical bounds. In parallel, a web application was developed to present the information and provide computational access via a web service. Designed specifically to accommodate high throughput mass spectrometry based approaches, lipids are organised into a hierarchy that reflects the variety in the structural resolution of lipid identifications. Additionally, cross-references to other lipid related resources and papers that cite specific lipids were used to annotate lipid records. The web application encompasses a browser for viewing lipid records and a 'tools' section where an MS1 search engine is currently implemented. LipidHome can be accessed at http://www.ebi.ac.uk/apweiler-srv/lipidhome.

Show MeSH
Related in: MedlinePlus