=Paper=
{{Paper
|id=Vol-1747/IP15_ICBO2016
|storemode=property
|title=uc_Milk: An Ontology for Scientifically-based Unambiguous Characterization of Mammalian Milk, their Composition and the Biological Processes Giving Rise to their Creation
|pdfUrl=https://ceur-ws.org/Vol-1747/IP15_ICBO2016.pdf
|volume=Vol-1747
|authors=Emeline Colet,Matthew Lange
|dblpUrl=https://dblp.org/rec/conf/icbo/ColetL16
}}
==uc_Milk: An Ontology for Scientifically-based Unambiguous Characterization of Mammalian Milk, their Composition and the Biological Processes Giving Rise to their Creation ==
https://ceur-ws.org/Vol-1747/IP15_ICBO2016.pdf
uc_Milk: An ontology for scientifically-based
unambiguous characterization of mammalian milks,
their composition and the biological processes giving rise to their creation
Emeline Colet Matthew Lange, PhD
Ecole Nationale Supérieure de Chimie de Paris Department of Food Science and Technology
Chimie ParisTech University of California Davis
Paris, FRANCE Davis, CA
emeline.colet@etu.chimie-paristech.fr mclange@ucdavis.edu
Abstract - Recent efforts in biological ontology go to great entities related to milk consumption and production (both as a
lengths to unambiguously categorize biological entities and food and as an ingredient in foods). These additional
phenomena of the natural world, as well as their classifications hold promise for uc_Milk ontology usability
relationships with each other. This paper illustrates the relative to traceability and trust in commercial milk and all milk
importance of unambiguously characterizing mammalian products, and provide a platform for improvement of processing
milk because milk is a complex mixture of many chemical and production techniques, information about milk distribution,
components and thus represents a key role in infant availability and choice, as well as increased health and well-
nourishment and development. In addition to the build of a being of consumers. uc_Milk maps directly to entities from
computable knowledge base around mammalian milk, several other ontologies. Yet because milk is often at the “leaf”
ontological modeling of this aspect of biology and chemistry end of existing ontologies as in the "Environment Ontology".
enable increased understanding of mammalian milk The "Uber Anatomy Ontology (Uberon)” and the "Gene
composition and the biological structures and biochemical Ontology" and "Vertebrate Taxonomy Ontology" respectively
processes giving rise to their creation. Utilizing unambiguous provide structures for mammary gland structures and
vocabularies to compare human milk with other mammalian development, the lactogenesis biological process, and formal
milks relative to the biological and behavioral survival mammalian phylogeny. uc_Milk also maps to the "Cell Ontology
challenges facing varied mammalian organisms and the (CL)" for the intracellular anatomical structures and processes.
phenotypic qualities each milk confers, is a fundamental goal uc_Milk is currently expanding feeding behaviors by mapping to
of this project. the burgeoning uc_Eating ontology as well as to anatomical
entities and the roles in the development of neural infant tissues
Keywords - mammalian milk composition; ontological in the NeuroBehavior Ontology. uc_Milk increases availability
modeling; biological processes of structured knowledge relative to milk.
One foundational design pattern for creating uc_Milk is an Lactation is the hallmark underlying biological force driving
ontology for unambiguous characterization of mammalian milks, the mother-infant dyad in Mammalia. The significant energetic
their composition and the biological processes giving rise to their and metabolic costs of lactation imposed to the mother suggests
creation. Available online at the GitHub website github.com/IC- that milk’s role in infant health extend well beyond simple
FOODS/uc_Milk, uc_Milk is part of a larger multi-ontology nutrition. Millennia of selective pressures on the mother-infant
framework [1] currently being housed within the International dyad, have conferred in milk a dual purpose: an optimal source
Center for Food Ontology Operability, Data, and Semantics. IC- of nutrients, and a delivery vehicle for bioactive agents. Milk is
FOODS at UC Davis [2]. Milk is at once, a consumable known as nature’s most complete food because of its complex
beverage, an ingredient at the heart of the dairy industry, and mixture of bioactive components and essential nutrients such as
often the sole nutritive source for infants--being both a source of protein, fat, carbohydrate, minerals, vitamins, and
dietary metabolites as well as a transport mechanism for physiologically active substances. Aside from nutritional values
xenobiotic agents. In all of its roles as a food/ingredient source, of milk, biologically active compounds such as casein and whey
milks are known to confer specific health phenotypes as they proteins have been found to be increasingly important for
interact with specific genotypes. Yet to date milk has received physiological and biochemical functions that have crucial
very limited attention in the world of ontological research. impacts on human metabolism and health. Accordingly, the
infant gut and its associated microbiota are adapted not only for
We used the Basic Formal Ontology as an upper ontology the utilization and absorption of milk macronutrients, but also to
because of its ubiquity in biological and biomedical ontologies, respond to non-nutritive, yet bioactive molecular entities.
for facilitating integration by way of meta-concepts. In addition Important non-nutritive, bioactive agents in human milk include
to characterizing the biological and biochemical structures and an astonishing high number of complex oligosaccharides, and a
processes related to mammalian milks, since milk is a plethora of glycoconjugated proteins and lipids. Complex
commodity as well as an essential biological fluid, uc_Milk prebiotic oligosaccharides are known to be present in domestic
ontology considers social, commercial, and environmental animal milks, yet are in low abundance relative to human milk, a
known source of prebiotic oligosaccharides with important to milk, pregnancy stage with biological modifications and
effects on human health. Characterization of these molecules, hormones, and lactation stage which is divided in four steps :
known as Human Milk Oligosaccharides or HMOs started in the mammogenesis, lactogenesis, galactopoiesis and involution. At
1960s, yet even today, their analysis remains a challenging task the same time, lactogenesis is classified as subclass of biological
due to the large number of structures and their structural process due to the secretory differentiation of mammary gland
complexity. No commercially viable processes for and the biological production of milk. Additionally, lactation
manufacturing these complex and important milk bioactives system described as subclass of exocrine system includes the
exist, making the third largest component of breast milk, biological functional anatomy of the lactating mammary gland
conspicuously absent in today’s infant formulas, weaning foods, and the biological transport and secretion pathways because
medical foods and everyday dairy products. Understanding the solutes can enter milk through both transcellular and paracellular
extent and types of oligosaccharides present in bovine milk is an routes. Transcellular routes are divided in four general pathways,
important step towards determining the feasibility of developing two for the secretion of endogenous substances and two other for
commercial sources. The identification, annotation and the transport of exogenous substances (Figure 2) [6]. The
characterization of oligosaccharides and other bioactive biological factors of milk production overlap with the
compounds in milk in is a necessary step to evaluate the
processes giving rise to their formation, and will enable future
scale-up processes for recovering these ingredients for
commercial applications.
The tremendous variation of milk compositions that occurs
among mammalians is one of the particularly interesting aspects
of lactation biology. As mammals include the largest animals of
the planet, a classification has been established: mammalians
have been separated into two major groups, placental and non-
placental mammals. Classification systems based on molecular
studies reveal three major groups or lineages of placental Figure 2 : Lactation system
mammals: Afrotheria, Xenarthra and Boreoeutheria which have
been divided in clades, superorders and orders [3] [4]. The aim breastfeeding behavior of uc_Eating ontology.
is to compare composition of a great number mammalian milk
with human milk based on fat, protein, sugar, vitamin, dry matter The second part of uc_Milk is industrial and food focused.
and energy content and to understand the influence of various uc_Milk provides structures in milk processing, milk process,
factors such as consumed diet, lactation time, habitat and many milk producing, milk production as well as food products : milk
others on milk composition [5]. Another important part of is involved in many dairy food products such as butter, cream, or
developing this ontology is to describe the processes giving rise cheese. Milk attributes are subclasses of food product and the
to milk creation. Indeed milk is a complex mixture whose milk sensory quality attribute overlap with the uc_Sense
composition reflects the activities of distinct secretion and ontology. The format of the ontology connects the subclasses of
transport processes of the mammary gland and mirrors the milk processing process and milk production process to the
differing nutritional requirements of mammalian mammary uc_Processing ontology. Furthermore, uc_Milk characterizes the
gland neonates [6]. To accomplish those main goals, uc_Milk composition of different mammalian milk as subclass of milk
covers two main points of view: on the one hand because milk is producing entity.
a complex biologically derived fluid, uc_Milk will serve basic
science but on the other hand, since milk is involved in many Using Protégé, with the streamlined interface and the
dairy products, this ontology is also designed to facilitate program's ability to add changes and import existing ontology
files improved the flow of classification and improved the
reproducibility of uc_Milk. This ontology is still at an early stage
so we are just beginning the process of adding axioms and we
have not yet tested this initial ontology. Sustainability plans for
the ontology will be developed once we receive initial feedback
from the community about how paths forward for integration
with related ontologies. Entity identifiers will be established after
feedback is received from ICBO participants, and integration
partners are identified.
REFERENCES
[1] Lange, M. C., Lemay, D. G., German, J. B. (2007). A multi-ontology
utilization in commercial and industrial foods. framework to guide agriculture and food towards diet and health. Journal
of the Science of Food and Agriculture, 87, 1427-1434.
Figure 1 : Milk components [2] Boulos, M. N. K., Yassine, A., Shirmohammadi, S., Namahoot, C. S,
Brücker, M. (2015). Towards an “Internet of Food”: Food Ontologies for
The first part of uc_Milk has breastmilk as starting point: as the Internet of Things. Future Internet, 7, 372-392.
mammary glandular fluid, milk supplies water and chemicals [3] Tarver, J.E. et al. (2016). The Interrelationships of Placental Mammals and
components to the neonate for his survival, proper development, the Limits of Phylogenetic Inference. Genome Biol Evol, 8 (2) : 330-344.
and vigorous growth (Figure 1). uc_Milk provides structures in [4] Langer, P. (2008). The phases of maternal investment in eutherian ammals.
three stages of life cycle: infant stage with breastfeeding thanks Zoology, 111 (2), 148-162.
[5] Skibiel, A.L., Downing, L.M., Orr, T.J, Hood, W.R. (2013). The evolution [6] Mc Manaman, J.L., Neuville, M.C. (2003). Mammary physiology and milk
of the nutrient composition of mammalian milks. Journal of Animal secretion. Advanced Drug Delivery Reviews, 55, 629–641.
Ecology, 82, 1254–1264.