| Problem | AP | BC | BM | BP | CM | EA | EB | FO | IM | LC | MD | ML | SA | SD | SW | TH | TM | TX | W2 | XM | Count |
|---|
| Education | 7 | | 3 | 1 | 1 | 1 | | 4 | 1 | 1 | 4 | | 4 | 8 | 6 | 2 | | 6 | 2 | 1 | 10 |
| Development methods | 4 | 1 | 1 | | 1 | | 1 | 2 | 1 | 1 | 1 | | 1 | 5 | 6 | 1 | 1 | 4 | 2 | 1 | 7 |
| Lack of common understanding of what is meant by an ontology | 2 | | 1 | | 1 | | | 2 | | 2 | 4 | 1 | 3 | 4 | 2 | 2 | 2 | 3 | 2 | 2 | 6 |
| Demonstrate utility | 4 | | 1 | | | | | 3 | | | | | 1 | 2 | 2 | 1 | | 3 | 2 | | 4 |
| Mappings among ontologies | 2 | | 2 | | 1 | | | 3 | | 1 | 2 | | 2 | 2 | 1 | 2 | 1 | 1 | | 1 | 4 |
| Developing consensus on a common foundation ontology | 2 | | 2 | | 2 | | | 2 | | 2 | 2 | | 1 | 2 | 2 | 2 | 1 | 3 | | 2 | 3 |
| Lack of an open, well-maintained clearinghouse for ontologies and related products and services that are enabled by them | 2 | 1 | | | 1 | | | 1 | | | | | | 1 | 2 | | 1 | | 1 | | 2 |
| Too many ontology standards and languages that are not compatible | 1 | | | | | | | 2 | | | 1 | | 1 | 2 | 2 | 1 | | 1 | | 1 | 2 |
| Complexity and cost | 1 | | | | | | | | | | | | | | | | | | | | 1 |
| Cooperation among different groups | 1 | | 1 | | 1 | | | | | | | | 1 | | 1 | | 1 | | 1 | | 1 |
| De-mystifying and simplifying ontologies and ontological terminology | | | | | | | | | | | | | | | | | | | 1 | | 1 |
| Developing, verifying and validating ontologies | | | | | | | | 1 | | | | | | 1 | 1 | | | | | | 1 |
| Lack of an identifying scheme for biomedical entities | | | 1 | | | | | | | | | | | | | | | | | | 1 |
| Lack of extensive ontology experience | | | 1 | | | | | 1 | | | | | | | 1 | | | | | | 1 |
| Lack of usable ontology language | | | 1 | | | | | 1 | | | | | | | 1 | | | | | | 1 |
| Missing predicates in tagging solutions | | | | | | | | | | | 1 | | | 1 | | | | | 1 | 1 | 1 |
| Navigation | 1 | | | | | | | | | | | | 1 | 1 | 1 | | | | | | 1 |
| Ontology has a bad reputation | | | | | | | | | | 1 | | | | | | | | | | | 1 |
| Overemphasis on formal logic | | | 1 | | | | | | | | | | | | 1 | | | | | | 1 |
| Scoping | 1 | | | | | | | | | | | | 1 | 1 | 1 | | | | | | 1 |
| Uncertainty | 1 | | 1 | | | | | 1 | | | | | | 1 | 1 | | | | | | 1 |