Jia Ren

The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and PSI-MOD as a post-translational modification reference. We illustrate its use in facilitating an alignment between PRO and Reactome protein entities. We also address issues of scalability, describing our first steps into the use of text mining to identify protein-related entities, the large-scale import of proteoform information from expert curated resources, and our ability to dynamically generate PRO terms. Web views for individual terms are now more informative about closely-related terms, including for example an interactive multiple sequence alignment. Finally, we describe recent improvement in semantic utility, with PRO now represented in OWL and as a SPARQL endpoint. These developments will further support the anticipated growth of PRO and facilitate discoverability of and allow aggregation of data relating to protein entities.

Changes in society lead to changes in science, changing its fundamental foundations - ideological and value, methodological and instrumental foundations. In turn, a change in the scientific paradigm leads to social change. A situation of this kind is especially evident in the socio-political sciences, since it is they who are more affected by social reality. The nature of postmodern societies is such that its economic component generates a huge number of subcultures, in the scientific world it is called "subcultural explosion." Postmodern societies are societies of permanent changes: consumer standards, moral values, political structure, and so on, repeatedly change during the life of one generation, significantly affect the search for the truth of science and its understanding. In the list of various questions of truth, its character, origin, postmodern departs from objective truth, therefore it becomes contextual and consensus. Theories are replaced by approaches, views, points of view, thoughts. Scientific concepts with their strict certainty change concepts, in which under the same name everyone puts their own meaning and essence. According to this, in postmodernism, not only the scientific paradigm as a model of scientific activity is changing, but the purpose of science, its understanding as a special activity with the search for truth, is changing. This implies a review of the attitude to the "organizational forms" of science, that is, the way in which scientific knowledge is disseminated to the professional scientific community to search for truth, which in its classical understanding no longer exists.