About PlantFAdb (previously PhyloFAdb)
The Seed Oil Fatty Acid (SOFA) database (http://sofa.mri.bund.de/) based at the Max Rubner Institute is a unique resource that presents data from >1400 publications (+ unpublished data) for >300 fatty acids and is based on analysis of ~7000 plant species. Building on SOFA, we have developed PlantFAdb as a tool to allow users to easily explore phylogenetic relationships between fatty acid structures and the plant species that produce them.
Overview of PlantFAdb
“Tree” displays the phylogenetic relationships between species that produce specific fatty acids, or groups of fatty acids. The initial overview displays plant orders and the wt% composition of a fatty acid reported for species within each order. Users can navigate to the level of family, genus and species by clicking on nodes in the phylogenetic tree. Clicking on bars in the graph leads to publications underlying the data.
“Fatty Acids” page presents the structures, MW, short-hand notation,
systematic and common names for over 450 fatty acids produced by plants.
Clicking on the structure presents links to other
databases and a list of publications that report the fatty acid and plants that contain the fatty acid.
- · Clicking on “Tree” from the Fatty Acid page presents a phylogenetic tree that displays the reported occurrence of the fatty acid within the plant kingdom.
“Plants” provides of list of >8000 plants included in the database, oil content of seeds (when available) and links to publications for the species. Clicking on a plant name leads to a graph showing the fatty acid composition and other data compiled from multiple publications. Clicking on the points in the graph leads to publications.
“Literature” provides a list of more than 3000 publications with data used in PlantFAdb. Clicking on an individual publication provides additional information including the plant species and the number of fatty acid data points for each. In addition there are approximately 700 tables of FA composition from unpublished studies, most of which were conducted at the Institute for Lipid Research, Münster, Germany.
Additions to SOFA that have been incorporated into PlantFAdb
Updated systematic names for
fatty acids. The primary systematic name used by PlantFAdb is based on the Chemical Abstract Service (CAS). In most cases a IUPAC systematic name is also provided on pages for individual fatty acids.
Chemical structures for fatty
acids (drawn based on systematic name by software at http://opsin.ch.cam.ac.uk/).
In cases where the double bond location or configuration or other aspects
of name are not specified, a structure is usually still provided.
Additional names, and common
names added (in most cases based on CAS)
Molecular weight and formula
added for most FA
CAS ID numbers added for
approximately 300 fatty acids.
Links to other chemical databases
such as PUBCHEM, LIPIDMAPS added
Machine readable chemical
notations added (SMILES, InChI, etc.).
Global search for all data.
Approximately 30% of plant names
in SOFA were updated (mainly Family names) based on information at the
Taxonomic Name Resolution Service (http://tnrs.iplantcollaborative.org/).
Common names of plants (English)
based on USDA (
.gov/) have been added for approximately
3000 species (in progress).
Titles added for more than 1700 references
Abstracts added for more than 1100 references
- Digital Object Identifier (DOI) added for approximately 900 references. In most cases this provides a link to the full text of the publication.
- Update of literature with ~150 publications from past 10 years (in progress)
- Survey of Chinese literature: (in progress). Data from ~1000 publications and from 6 books including 1344 species from 125 families with 4300 fatty acid profiles.
PlantFAdb does not include data from SOFA for tocopherols, sterols, and triacylglycerol structures. In addition, some remarks provided by SOFA in FA analysis tables are not yet incorporated and some FA data is not yet incorporated mostly because the units reported for the analysis are uncertain. Links to original SOFA website tables are provided when available. It is likely that some mistakes have been made during incorporation of SOFA information into PlantFAdb. Please notify John Ohlrogge if you find these.
Contributors to PlantFAdb
John Ohlrogge, Nick Thrower, Curtis Wilkerson, Melissa Baxter, Weili Yang, Kate McGlew, Jinjie Liu, Devin Higgins, at Michigan State University, USA
Bertrand Matthaus at Max Rubner-Institut, Detmold, Germany
Meng Zhang, Xiaojun Cheng and Changsheng Li at Northwest A&F University, Shaanxi, China
Vandana Mhaske, Independent Biotechnology Professional, Pune, India
Basil Shorrosh, Biotechnology Professional, Fort Collins, Colorado, USA
Ajay W Tumaney at CSIR-Central Food Technological Research Institute, Mysore, India