=Paper=
{{Paper
|id=Vol-1747/IP30_ICBO2016
|storemode=property
|title=Supporting Database Annotations and Beyond with the Evidence & Conclusion Ontology (ECO)
|pdfUrl=https://ceur-ws.org/Vol-1747/IP30_ICBO2016.pdf
|volume=Vol-1747
|authors=Marcus Chibucos,Suvarna Nadendla,James Munro,Elvira Mitraka,Dustin Olley,Nicole Vasilevsky,Matthew Brush,Michelle Giglio
|dblpUrl=https://dblp.org/rec/conf/icbo/ChibucosNMMOVBG16
}}
==Supporting Database Annotations and Beyond with the Evidence & Conclusion Ontology (ECO) ==
https://ceur-ws.org/Vol-1747/IP30_ICBO2016.pdf
Supporting database annotations and beyond with the
Evidence & Conclusion Ontology (ECO)
Marcus C. Chibucos1*, Suvarna Nadendla1, James B. Munro1, Elvira Mitraka1,
Dustin Olley1, Nicole A. Vasilevsky2, Matthew H. Brush2, Michelle Giglio1
1
Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD United States of America
2
Ontology Development Group, Library, Oregon Health & Science University, Portland, OR United States of America
*Corresponding author: mchibucos@som.umaryland.edu; (410) 705-0885; 801 W. Baltimore St., Baltimore, MD, 21201
Abstract—The Evidence & Conclusion Ontology (ECO) is a supported by systematically describing evidence. Because ECO
community standard for summarizing evidence in scientific terms are ontology terms, they contain standard definitions and
research in a controlled, structured way. Annotations at the are networked using defined relationships. Thus, associating
world's most frequented biological databases (e.g. model research data with descriptions of evidence using ECO can
organisms, UniProt, Gene Ontology) are supported using ECO
allow, for example, faceted queries of large datasets and
terms. ECO describes evidence derived from experimental and
computational methods, author statements curated from the implementations of customized quality control mechanisms.
literature, inferences drawn by curators, and other types of
II. ESSENTIALS OF ECO
evidence. Here, we describe recent ECO developments and
collaborations, most notably: (i) a new ECO website containing A. Basic ECO structure
user documentation, up-to-date news, and visualization tools; (ii)
improvements to the ontology structure; (iii) implementing logic
As depicted in Fig. 1, ECO comprises two high-level classes,
via an ongoing collaboration with the Ontology for Biomedical ‘evidence’ (ECO:0000000) & ‘assertion method’ (ECO:0000217).
Investigations (OBI); (iv) addition of numerous experimental The definition of ‘evidence’ is “a type of information that is used
evidence types; and (v) addition of new evidence classes describing to support an assertion” and ‘assertion method’ is defined as “a
computationally derived evidence. Due to its utility, popularity, means by which a statement is made about an entity” [1].
and simplicity, ECO is now expanding into realms beyond the Together ‘evidence’ and ‘assertion method’ can be combined to
protein annotation community, for example the biodiversity and describe both the support for an assertion and whether the
phenotype communities. As ECO continues to grow as a resource, assertion was generated by manual or automatic means. ECO
we are seeking new users and new use cases, with the hope that terms descend mainly from the ‘evidence’ hierarchy. However,
ECO will continue to be a broadly used and easy-to-implement ‘evidence’ leaf terms are related to the ‘assertion method’ terms
community standard for representing evidence in diverse by the ‘used_in’ relationship. Thus, one can assert not only what
biological applications. Feel free to visit two ECO-sponsored evidence is used to support a particular assertion, but also
workshops at ICBO 2016 to learn more: 1. “An introduction to the whether the assertion was made by a human being or a computer
Evidence and Conclusion Ontology and representing evidence in (Fig. 1).
scientific research” and 2. “OBI-ECO Interactions & Evidence”.
B. Traditional uses of ECO
Keywords—annotation; biodiversity; biomedical investigation; Some traditional example applications of ECO are found in
conclusion; confidence; curation; evidence; experimental evidence; uses by the Gene Ontology [3]: (a) hierarchical ECO classes are
inference; provenance; sequence similarity.
used to support structured data queries; (b) when a protein is
I. INTRODUCTION annotated based on sequence similarity to another annotated
protein, the identity of that protein must be recorded in the
The Evidence & Conclusion Ontology (ECO) [1] summarizes annotation file along with the evidence from ECO; (c) quality
types of scientific evidence associated with biological research. control assessment can be enforced by only allowing certain
Evidence can arise from laboratory experiments, computational annotations to terms from a given ontology to be supported by
methods, manual literature curation, or other means. particular evidence types—lest such annotations be flagged for
Researchers, biocurators, and database managers use this review; and (d) circular annotations based on computational
evidence to justify their conclusions and support resulting predictions alone can be determined, and thus avoided. In the
assertions, for example stating that a given protein has a ways described above, ECO has been used by many databases
(e.g. UniProt, model organisms, Gene Ontology, et cetera) to
particular function.
support protein annotations. However, ECO has additional uses.
Summarizing evidence with ECO allows projects such as the
UniProt-Gene Ontology Annotation (UniProt- GOA) project [2] C. Recent ECO term development
to manage large volumes of annotations in a convenient fashion, A growing number of resources/applications use ECO (more
as both data management and query applications are than 40 of which we are aware). ECO has recently expanded its
This work is supported by funding from the National Science Foundation
Division of Biological Infrastructure under award number 1458400.
Fig. 1. ECO root classes and combinatorial terms. Leaf terms depicted are logically defined as the ‘evidence’ parent class (‘match
to InterPro member signature evidence’) related to the ‘assertion method’ class via the ‘used_in’ relationship (gray boxes).
evidence representation through collaborations with many Specific examples of these will be addressed at the ICBO 2016
groups, for example: IntAct [4] (biological system workshop titled “An introduction to the Evidence and
reconstruction), CollecTF [5] (motif prediction), Ontology of Conclusion Ontology and representing evidence in scientific
Microbial Phenotypes [6] (microbial assays), Planteome research” (workshop W11) and new users and adopters are
(http://planteome.org; genotype-phenotype associations), Gene especially encouraged to attend to learn more.
Ontology [3] (logical inference & synapse research techniques), ACKNOWLEDGMENT
SwissProt [7] (diverse experimental assays), and UniProt [2,7] The authors acknowledge the Ontology for Biomedical
(detection techniques). Investigations (OBI) Consortium and, in particular, Bjoern
III. THE FUTURE OF ECO Peters for ongoing collaboration with ECO. We thank Christian
J. Stoeckert, Jr. and Jie Zheng for co-organizing the ICBO 2016
A. Increasing the logic within ECO workshop W08 titled “OBI-ECO Interactions & Evidence.”
In May 2016, 14 people met in person at the Institute for
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