diff --git a/edam_manager.py b/edam_manager.py new file mode 100644 index 00000000..a2acc70a --- /dev/null +++ b/edam_manager.py @@ -0,0 +1,57 @@ + + +class edam_manager(object): + + def __init__(self): + # ontology parsing happens here + pass + + def get_terms_by_name(self, name): + """ + query for ontological terms by name + :param name: str + :return: collection of term + """ + pass + + def common_ancestors(self, term1, term2): + """ + returns the terms that are the least common ancestors of the given two terms + :param term1: + :param term2: + :return: collection of term + """ + pass + + def is_placeholder(self, term): + """ + checks if a term is a real term or a placeholder created for structuring purposes. + :param term: + :return: True if the term is an organisational entity (e.g., alignment, 'phylogenetic data') + or False if it is a real term (e.g., 'sequence alignment', 'phylogenetic tree'). + """ + pass + + def format2data(self, term): + """ + given a format term returns the corresponding data terms, e.g. given 'newick' returns 'phylogenetic tree'. + :param term: format term + :return: collection of data term + """ + pass + + def get_description(self, term): + """ + returns the term description + :param term: + :return: str + """ + pass + + def get_term_by_id(self, id): + """ + query for an ontological term by id + :param id: str + :return: term + """ + pass