There are several methodologies available on the literature for developing an ontology from scratch such as Ushold & King, Grüninger & Fox, 101, KACTUS, On-To-Knowledge, METHONTOLOGY, KUP, and DILIGENT. For extracting concepts from text documents, some colleagues developed a work (A Linguistic Approach to Conceptual Modeling with Semantic Types and OntoUML) based on R. M. W. Dixon (see A Semantic Approach to English Grammar: https://www.researchgate.net/publication/239720225_A_Semantic_Approach_to_English_Grammar?ev=pub_cit ).

Article A Semantic Approach to English Grammar

Firstly, I encourage you to look for existing ontologies to solve your problem and check if you can reuse them or not, because there are multiple ongoing projects focused on ontology development and it is possible that you do not need to build your own model. As an example, for the biomedical domain there is a reference repository called BioPortal (bioportal.bioontology.org), where you can access more than 300 biomedical ontologies and reuse them.

If you are sure that you need to develop your own ontology instead of reusing existing ones, there is a recent work that may be useful for you [1]. It is about creating a knowledge base from a Biology textbook.

[1] http://ontolog.cim3.net/file/resource/presentation/VinayChaudhri_20130627/KB-Bio-101--VinayChaudhri_20130627.pdf

I would also recommend you to check another useful ontology development methodology proposed by Noy and McGuinness in [1], which is an iterative ontology development process consisting of seven steps.

[1]

Natalya F. Noy and Deborah L. Mcguinness. Ontology development 101: A guide to creating your first ontology. Development, 32(1):1–25, 2000

If your input is textual documents, you need to do text processing techniques. For eg. to find all the classes for your ontology Do Named entity recognition and find out the concepts.