Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science

Within clinical, biomedical, and translational science, an increasing number of projects are adopting graphs for knowledge representation. Graph‐based data models elucidate the interconnectedness among core biomedical concepts, enable data structures to be easily updated, and support intuitive queries, visualizations, and inference algorithms. However, knowledge discovery across these “knowledge graphs” (KGs) has remained difficult. Data set heterogeneity and complexity; the proliferation of ad hoc data formats; poor compliance with guidelines on findability, accessibility, interoperability, and reusability; and, in particular, the lack of a universally accepted, open‐access model for standardization across biomedical KGs has left the task of reconciling data sources to downstream consumers. Biolink Model is an open‐source data model that can be used to formalize the relationships between data structures in translational science. It incorporates object‐oriented classification and graph‐oriented features. The core of the model is a set of hierarchical, interconnected classes (or categories) and relationships between them (or predicates) representing biomedical entities such as gene, disease, chemical, anatomic structure, and phenotype. The model provides class and edge attributes and associations that guide how entities should relate to one another. Here, we highlight the need for a standardized data model for KGs, describe Biolink Model, and compare it with other models. We demonstrate the utility of Biolink Model in various initiatives, including the Biomedical Data Translator Consortium and the Monarch Initiative, and show how it has supported easier integration and interoperability of biomedical KGs, bringing together knowledge from multiple sources and helping to realize the goals of translational science.

A broad-spectrum cloning vector that exists as both an integrated element and a free plasmid in Chlamydia trachomatis

Plasmid transformation of chlamydiae has created new opportunities to investigate host-microbe interactions during chlamydial infections; however, there are still limitations. Plasmid transformation requires a replicon derived from the native Chlamydia plasmid, and these transformations are species-specific. We explored the utility of a broad host-range plasmid, pBBR1MCS-4, to transform chlamydiae, with a goal of simplifying the transformation process. The plasmid was modified to contain chromosomal DNA from C. trachomatis to facilitate homologous recombination. Sequences flanking incA were cloned into the pBBR1MCS-4 vector along with the GFP:CAT cassette from the pSW2-GFP chlamydial shuttle vector. The final plasmid construct, pBVR2, was successfully transformed into C. trachomatis strain L2-434. Chlamydial transformants were analyzed by immunofluorescence microscopy and positive clones were sequentially purified using limiting dilution. PCR and PacBio-based whole genome sequencing were used to determine if the plasmid was maintained within the chromosome or as an episome. PacBio sequencing of the cloned transformants revealed allelic exchange events between the chromosome and plasmid pBVR2 that replaced chromosomal incA with the plasmid GFP:CAT cassette. The data also showed evidence of full integration of the plasmid into the bacterial chromosome. While some plasmids were fully integrated, some were maintained as episomes and could be purified and retransformed into E. coli. Thus, the plasmid can be successfully transformed into chlamydia without a chlamydial origin of replication and can exist in multiple states within a transformed population.

Inter-species lateral gene transfer focused on the Chlamydia plasticity zone identifies loci associated with immediate cytotoxicity and inclusion stability

Chlamydia muridarum actively grows in murine mucosae and is a representative model of human chlamydial genital tract disease. In contrast, C. trachomatis infections in mice are limited and rarely cause disease. The factors that contribute to these differences in host adaptation and specificity remain elusive. Overall genomic similarity leads to challenges in the understanding of these significant differences in tropism. A region of major genetic divergence termed the plasticity zone (PZ) has been hypothesized to contribute to the host specificity. To evaluate this hypothesis, lateral gene transfer was used to generate multiple hetero-genomic strains that are predominately C. trachomatis but have replaced regions of the PZ with those from C. muridarum. In vitro analysis of these chimeras revealed C. trachomatis-like growth as well as poor mouse infection capabilities. Growth-independent cytotoxicity phenotypes have been ascribed to three large putative cytotoxins (LCT) encoded in the C. muridarum PZ. However, analysis of PZ chimeras supported that gene products other than the LCTs are responsible for cytopathic and cytotoxic phenotypes. Growth analysis of associated chimeras also led to the discovery of an inclusion protein, CTL0402 (CT147), and homolog TC0424, which was critical for the integrity of the inclusion and preventing apoptosis.

P–739 Fertility and its Preservation: Comparative Analysis about the Knowledge between Two Populations of Doctors and Health Professionals from Argentina and the United States

Study question

Is there any difference in the knowledge that doctors and health professionals from Córdoba (Argentina) and South Carolina (USA) have about fertility preservation or about when it should be applied?

Summary answer

Both populations have enough knowledge about some aspects of fertility preservation, but its training must be improved so they can give adequate counseling

What is known already

During the last decades, it has been observed that more young individuals need/decide to preserve fertility, whether for social or medical reasons. This presents a new challenge for the medical community, since, faced with this situation, it is important that society in general has access to information about fertility and the possibilities of preserving it, if necessary. To this end, it is essential that doctors and other health professionals have valid knowledge of the subject and are able to communicate it to their patients.

Study design, size, duration

Descriptive quantitative study. A total of 721 answers were obtained, 88.7% from Argentina and 11.3% from the United States. 28.43% (205) were doctors and 71.57% (516) were other health professionals.

Participants/materials, setting, methods

A closed-ended questionnaire of 20 questions was designed (segmentation and aspects about fertility preservation) and distributed to society through social networks. The survey was answered by people from Córdoba (Argentina) and South Carolina (US), of both sexes and different age, educational and socioeconomic levels. Only those with a medical degree or involved in some medical-related activity were selected. All answers were collected through SurveyMonkey and analyzed using calculation programs and statistical tools (Excel–2016, Statistica 8.0).

Main results and the role of chance

Data showed percentages of correct answers greater than 70% in all groups for the questions that analyze what factors can affect fertility, what situations can determine the need to preserve it, and what is the appropriate age for a woman to cryopreserve her eggs. On average, 82.4% of doctors and 72.87% of other health professionals know when it is the right time for patients diagnosed with cancer to receive information about the possibility of preserving their fertility. However, on average between both countries, only 34.63% of doctors has information about the legal medical coverage of their patients, while the 39.51% is completely unaware of their country’s laws. Finally, the percentages of professionals who do not know what material can be cryopreserved in girls who need to undergo oncological treatments reach 46.34 and 64.33% (doctors and other health professionals respectively).

Limitations, reasons for caution

The comparison between the two countries may be challenged by the inequality in the response rate to the survey. However, even the smaller number of responses obtained in the USA is sufficient to obtain valid conclusions.

Wider implications of the findings: Both populations have sufficient information about factors which affect fertility and its preservation, especially in cancer situations. Misinformation in health personnel about these aspects directly affects possibilities of achieving future pregnancies for patients. Continuous updating and guidance should be a priority, as well as information dissemination and adequate medical counseling.

Trial registration number

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Intrathecal administration of 131I radiolabelled monoclonal antibody as a treatment for neoplastic meningitis

Fifteen patients with neoplastic meningitis received a single intrathecal injection of between 11 and 60 mCi of a 131I radiolabelled monoclonal antibody (MoAb), chosen for its immunoreactivity to tumour. Major toxicity was manifest as nausea, vomiting and headache (7/15 patients), reversible bone marrow suppression (3/8 patients) and seizures (2/15 patients). Nine patients were evaluable for either a tumour or clinical response. Six of these demonstrated an event-free response that was maintained for periods of between 7 and 26 months.