# HoloOLIGO corpus, a manually annotated text dataset supporting schema-based relational information extraction for mammalian milk oligosaccharide diversity pattern comprehension

Mathilde Rumeau, Robert Bossy, Clara Sauvion, Valentin Loux, Mouhamadou Ba, Christelle Knudsen, Sylvie Combes, Claire Nédellec, Louise Deléger

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Mathilde Rumeau, Robert Bossy, Clara Sauvion, Valentin Loux, Mouhamadou Ba, et al.. HoloOLIGO corpus, a manually annotated text dataset supporting schema-based relational information extraction for mammalian milk oligosaccharide diversity pattern comprehension. Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM), Jun 2024, Toulouse, France. hal-04666797

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Submitted on 2 Aug 2024

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Distributed under a Creative Commons Attribution 4.0 International License
# HoloOLIGO corpus, a manually annotated text dataset supporting schema-based relational information extraction for mammalian milk oligosaccharide diversity pattern comprehension

Mathilde Rumeau¹, Robert Bossy², Clara Sauvion², Valentin Loux²,³, Mouhamadou Ba²,³, Christelle Knudsen¹, Sylvie Combes¹, Claire Nédellec² and Louise Deléger²

¹GenPhySE, INRAE, Université de Toulouse, 31326 Castanet Tolosan France ; ²Université Paris-Saclay, INRAE, MalAGE, Jouy-en-Josas, France ; ³Université Paris-Saclay, INRAE, BioinfOmics, MIGALE Bioinformatics Facility, Jouy-en-Josas, France

## Biological question

Milk oligosaccharides (MOs), highly structural complex molecules, are widely studied for their benefits on health. Functions of MO seem to be related to their structural motifs. However, MOs composition varies widely based on:

- ☐ Species

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- ☐ Genetic

- ☐ Maternal physiology

- ☐ Lactation stage

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- ☐ Geography

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**What is the biological significance of variations in MO profiles ?**

Data on associate or causal variability of the MO structure pattern are spread in an increasing volume of scientific articles that must be considered to understand the implications of such diversity on health.

## Automatic Natural Language Processing methods

are able to deal with the increasing number of publications

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## Extraction question: unstructured data to structured information

Milk oligosaccharides extraction

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- Lacto-N-Tetraose [1]

- LNT [2]

- Gal(β1-3)GlcNAc(β1-3)Gal(β1-4)Glc [3]

- 3_1_0_0_0 [4]

## Creation of a complex annotation schema to offer a relevant and valuable basis for modeling the MO diversity pattern

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To answer the biological question, identification of:

- 14 relevant entities

- 10 binary relations

- N-ary relations to link the extracted entities

Selection of 3 external semantic resources and creation of 4 proprietary glossaries to formalize the extracted entities from the raw text to a generic class

*MilkOligoThesaurus [5]: 245 MO structures and 22 descriptive columns to normalize MO

- ☐ Name

- ☐ Chemical information

- ☐ Abbreviation

- ☐ Synonyms

- ☐ Link to chemical database

- ☐ DOI sources

## Creation of a corpus of manually annotated texts used to train and evaluate named entity recognition, and relation extraction tools

Corpus selection of 30 relevant abstract and full text

Annotation guideline writing

Manual annotation with AlvisAE tool

PubMed

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Relative quantification

NCBI:txid9913

Relative quantification

Lactation stage

Together, 3'- and 6'-sialyllactose account for more than 50 % of the total oligosaccharides present in bovine colostrum

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## First results

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Percentage of occurrence of each entity among the 3 606 entities extracted

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Occurrence of each type of binary relations extracted

## Perspectives

- ☐ Training and evaluation of the automatic extraction methods

- ☐ Development of a MO reference database of the diversity of the structures identified among all mammalian species automatically extracted from the bibliography

## References

1. Remoroza CA, Liang Y, Mak TD, Mirokhin Y, Sheetlin SL, Yang X, et al. Increasing the Coverage of a Mass Spectral Library of Milk Oligosaccharides Using a Hybrid-Search-Based Bootstrapping Method and Milks from a Wide Variety of Mammals. Anal Chem. 4 août 2020;92(15):10316-26.

2. Aldredge DL, Geronimo MR, Hua S, Nwosu CC, Lebrilla CB, Barile D. Annotation and structural elucidation of bovine milk oligosaccharides and determination of novel fucosylated structures. Glycobiology. juin 2013;23(6):664-76.

3. Albrecht S, Lane JA, Mariño K, Al Busadah KA, Carrington SD, Hickey RM, et al. A comparative study of free oligosaccharides in the milk of domestic animals. Br J Nutr. 14 avr 2014;111(7):1313-28.

4. Trevisi P, Luise D, Won S, Salcedo J, Bertocchi M, Barile D, et al. Variations in porcine colostrum oligosaccharide composition between breeds and in association with sow maternal performance. JOURNAL OF ANIMAL SCIENCE AND BIOTECHNOLOGY. 12 mars 2020;11(1).

5. Rumeau M, Fenaille F, Girard A, Loux V, Ba M, Nédellec C, et al. MilkOligoThesaurus, a dataset of mammalian milk oligosaccharide synonyms. Data in Brief. juin 2024;54:110404.

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