Editing Semantic similarity (section)

=== In biomedical informatics ===
Semantic similarity measures have been applied and developed in biomedical ontologies.<ref>{{cite journal|last1=Guzzi|first1=Pietro Hiram|first2=Marco |last2=Mina |first3=Mario|last3= Cannataro|first4= Concettina |last4=Guerra|title=Semantic similarity analysis of protein data: assessment with biological features and issues|journal=Briefings in Bioinformatics|year=2012|volume=13|pages=569–585|issue=5|doi=10.1093/bib/bbr066|pmid=22138322|doi-access=free}}</ref><ref name="ReferenceA">{{cite journal |last1=Benabderrahmane|first1=Sidahmed|last2=Smail Tabbone|first2=Malika|last3=Poch|first3=Olivier |last4=Napoli|first4=Amedeo|last5=Devignes|first5=Marie-Domonique. |title=IntelliGO: a new vector-based semantic similarity measure including annotation origin |journal=BMC Bioinformatics|volume=11 |pages=588 |year=2010 |pmid=21122125 |doi=10.1186/1471-2105-11-588 |pmc=3098105 |doi-access=free }}</ref>
They are mainly used to compare [[genes]] and [[proteins]] based on the similarity of their functions<ref>{{cite journal | last1 = Chicco | first1 = D | last2 = Masseroli | first2 = M | year = 2015 | title = Software suite for gene and protein annotation prediction and similarity search | journal = IEEE/ACM Transactions on Computational Biology and Bioinformatics | volume = 12 | issue = 4 | pages = 837–843 | doi=10.1109/TCBB.2014.2382127 | pmid = 26357324 | hdl = 11311/959408 | s2cid = 14714823 | url = https://doi.org/10.1109/TCBB.2014.2382127 | hdl-access = free }}
</ref> rather than on their [[sequence similarity]],
but they are also being extended to other bioentities, such as diseases.<ref>{{cite journal |last1=Köhler |first1=S |last2=Schulz |first2=MH |last3=Krawitz |first3=P |last4=Bauer |first4=S |last5=Dolken |first5=S |last6=Ott |first6=CE |last7=Mundlos |first7=C |last8=Horn |first8=D |last9=Mundlos |first9=S |last10=Robinson |first10=Peter N. |title=Clinical diagnostics in human genetics with semantic similarity searches in ontologies |journal=American Journal of Human Genetics |volume=85 |issue=4 |pages=457–64 |year=2009 |pmid=19800049 |pmc=2756558 |doi=10.1016/j.ajhg.2009.09.003|display-authors=8 }}</ref>

These comparisons can be done using tools freely available on the web:
* ProteInOn can be used to find interacting proteins, find assigned GO terms and calculate the functional semantic similarity of [[UniProt]] proteins and to get the information content and calculate the functional semantic similarity of GO terms.<ref>{{cite web|url=http://xldb.fc.ul.pt/biotools/proteinon/|title=ProteInOn}}</ref>
* CMPSim provides a functional similarity measure between chemical compounds and metabolic pathways using [[ChEBI]] based semantic similarity measures.<ref>{{cite web|url=http://xldb.di.fc.ul.pt/biotools/cmpsim/|title=CMPSim}}</ref>
* CESSM provides a tool for the automated evaluation of GO-based semantic similarity measures.<ref>{{cite web|url=http://xldb.fc.ul.pt/biotools/cessm/|title=CESSM}}</ref>