LIPID MAPS online tools for lipid research

The LIPID MAPS consortium has developed a number of online tools for performing tasks such as drawing lipid structures and predicting possible structures from mass spectrometry (MS) data. A simple online interface has been developed to enable an end-user to rapidly generate a variety of lipid chemical structures, along with corresponding systematic names and ontological information. The structure-drawing tools are available for six categories of lipids: (i) fatty acyls, (ii) glycerolipids, (iii) glycerophospholipids, (iv) cardiolipins, (v) sphingolipids and (vi) sterols. Within each category, the structure-drawing tools support the specification of various parameters such as chain lengths at a specific sn position, head groups, double bond positions and stereochemistry to generate a specific lipid structure. The structure-drawing tools have also been integrated with a second set of online tools which predict possible lipid structures from precursor-ion and product-ion MS experimental data. The MS prediction tools are available for three categories of lipids: (i) mono/di/triacylglycerols, (ii) glycerophospholipids and (iii) cardiolipins. The LIPID MAPS online tools are publicly available at www.lipidmaps.org/tools/

Metabolomics Workbench: An International Repository for Metabolomics Data and Metadata, Metabolite Standards, Protocols, Tutorials and Training, and Analysis Tools

The Metabolomics Workbench, available at www.metabolomicsworkbench.org, is a public repository for metabolomics metadata and experimental data spanning various species and experimental platforms, metabolite standards, metabolite structures, protocols, tutorials, and training material and other educational resources. It provides a computational platform to integrate, analyze, track, deposit and disseminate large volumes of heterogeneous data from a wide variety of metabolomics studies including mass spectrometry (MS) and nuclear magnetic resonance spectrometry (NMR) data spanning over 20 different species covering all the major taxonomic categories including humans and other mammals, plants, insects, invertebrates and microorganisms. Additionally, a number of protocols are provided for a range of metabolite classes, sample types, and both MS and NMR-based studies, along with a metabolite structure database. The metabolites characterized in the studies available on the Metabolomics Workbench are linked to chemical structures in the metabolite structure database to facilitate comparative analysis across studies. The Metabolomics Workbench, part of the data coordinating effort of the National Institute of Health (NIH) Common Fund\u27s Metabolomics Program, provides data from the Common Fund\u27s Metabolomics Resource Cores, metabolite standards, and analysis tools to the wider metabolomics community and seeks data depositions from metabolomics researchers across the world

ClassyFire: automated chemical classification with a comprehensive, computable taxonomy

Additional file 5. Use cases. Text-based search on the ClassyFire web server. (A) Building the query. (B) Sparteine, one of the returned compounds

Revascularisation therapies improve the outcomes of ischemic stroke patients with atrial fibrillation and heart failure

Background: Atrial fibrillation (AF) and heart failure (HF) carry a poor prognosis in acute ischaemic stroke (AIS). The impact of revascularisation therapies on outcomes in these patients is not fully understood.  Method: National Inpatient Sample (NIS) AIS admissions (January 2004–September 2015) were included (n = 4,597,428). Logistic regressions analysed the relationship between exposures (neither AF nor HF-reference, AF-only, HF-only, AF + HF) and outcomes (in-hospital mortality, length-of-stay >median and moderate-to-severe disability on discharge), stratifying by receipt of intravenous thrombolysis (IVT) or endovascular thrombectomy (ET). Results: 69.2% patients had neither AF nor HF, 16.5% had AF-only, 7.5% had HF-only and 6.7% had AF + HF. 5.04% and 0.72% patients underwent IVT and/or ET, respectively. AF-only and HF-only were each associated with 75–85% increase in the odds of in-hospital mortality. AF + HF was associated with greater than two-fold increase in mortality. Patients with AF-only, HF-only or AF + HF undergoing IVT had better or at least similar in-hospital outcomes compared to their counterparts not undergoing IVT, except for prolonged hospitalisation. Patients undergoing ET with AF-only, HF-only or AF + HF had better (in-hospital mortality, discharge disability, all-cause bleeding) or at least similar (length-of-stay) outcomes to their counterparts not undergoing ET. Compared to AIS patients without AF, AF patients had approximately 50% and more than two-fold increases in the likelihood of receiving IVT or ET, respectively. Conclusions: We confirmed the combined and individual impact of co-existing AF or HF on important patient-related outcomes. Revascularisation therapies improve these outcomes significantly in patients with these comorbidities

LMSD: LIPID MAPS structure database

The LIPID MAPS Structure Database (LMSD) is a relational database encompassing structures and annotations of biologically relevant lipids. Structures of lipids in the database come from four sources: (i) LIPID MAPS Consortium's core laboratories and partners; (ii) lipids identified by LIPID MAPS experiments; (iii) computationally generated structures for appropriate lipid classes; (iv) biologically relevant lipids manually curated from LIPID BANK, LIPIDAT and other public sources. All the lipid structures in LMSD are drawn in a consistent fashion. In addition to a classification-based retrieval of lipids, users can search LMSD using either text-based or structure-based search options. The text-based search implementation supports data retrieval by any combination of these data fields: LIPID MAPS ID, systematic or common name, mass, formula, category, main class, and subclass data fields. The structure-based search, in conjunction with optional data fields, provides the capability to perform a substructure search or exact match for the structure drawn by the user. Search results, in addition to structure and annotations, also include relevant links to external databases. The LMSD is publicly available a

Challenging Practices : Experiences from community and individual living lab approaches

Peer reviewe

LipidFinder on LIPID MAPS: peak filtering, MS searching and statistical analysis for lipidomics

Summary We present LipidFinder online, hosted on the LIPID MAPS website, as a liquid chromatography/mass spectrometry (LC/MS) workflow comprising peak filtering, MS searching and statistical analysis components, highly customized for interrogating lipidomic data. The online interface of LipidFinder includes several innovations such as comprehensive parameter tuning, a MS search engine employing in-house customized, curated and computationally generated databases and multiple reporting/display options. A set of integrated statistical analysis tools which enable users to identify those features which are significantly-altered under the selected experimental conditions, thereby greatly reducing the complexity of the peaklist prior to MS searching is included. LipidFinder is presented as a highly flexible, extensible user-friendly online workflow which leverages the lipidomics knowledge base and resources of the LIPID MAPS website, long recognized as a leading global lipidomics portal

Comprehensive Open Access Dataset of Sustainable Energy Consumption Initiatives (SECIs) : Deliverable 2.3

This document (ENERGISE D2.3) provides a background report on the process and result of developing and constructing a comprehensive open access dataset of sustainable energy consumption initiatives (SECIs) that have been collected and assessed as part of Work Package 2 (WP2) in ENERGISE. The dataset is designed as a map that is intended to be a user-friendly device that provides an overview of sustainable energy consumption initiatives (SECIs) in Europe. In particular, the map shows the variety in scope, content and approach in the identified SECIs