During most of the 1990s, a linguistic chasm divided the worlds of flies, worms, mice, and other model organisms. People in one world remained largely ignorant about related genes and proteins being studied in the others, in part because each group stored data using its own peculiar vocabulary. Even within a single organism, a search for genes involved in "translation" might not pull up those described using the term "protein synthesis," and vice versa.
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Like human languages, each ontology has a slightly different structure. But, the GO is a good model for how the languages are formed. Each term in the ontology has an identification number and a definition. For example, the term "aging" has the identifier GO:0016280 and the definition: "The inherent decline over time, from the optimal fertility and viability of early maturity that culminates in death and may be preceded by other indications such as sterility."
The definition may include synonyms, allowing a search for "translation" to pull up entries using the term "protein synthesis" instead, and terms are defined as being a "cellular_component," "molecular_function," or "biological_process." Aging is defined as a biological_process. Each term can also be related to other terms through the relations is_a and part_of. Thus, Aging is_a Development (GO:0007275) and is part_of Death (GO:0016265).
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The end result of this linguistic tinkering is something that remains largely invisible to the bench scientist. He or she simply knows that by entering a search term such as Aging into FlyBase, the database will retrieve all gene products that are defined as being involved in that process. And all the terms are in what appears to be plain English. In fact, inclusion in the OBO requires that the terms and their associated definitions be clear to the reader.
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