Stakeholders in software projects use issue trackers like JIRA or Bugzilla to capture and manage issues, including requirements, feature requests, and bugs. To ease issue navigation and structure project knowledge, stakeholders manually connect issues via links of certain types that reflect different dependencies, such as Epic-, Block-, Duplicate-, or Relate- links. Based on a large dataset of 16 JIRA repositories, we study the commonalities and differences in linking practices and link types across the repositories. We then investigate how state-of-the-art machine learning models can predict common link types. We observed significant differences across the repositories and link types, depending on how they are used and by whom. Additionally, we observed several inconsistencies, e.g., in how Duplicate links are used. We found that a transformer model trained on titles and descriptions of linked issues significantly outperforms other optimized models, achieving an encouraging average macro F1-score of 0.64 for predicting nine popular link types across all repositories (weighted F1-score of 0.73). For the specific Subtask- and Epic- links, the model achieves top F1-scores of 0.89 and 0.97, respectively. If we restrict the task to predict the mere existence of links, the average macro F1-score goes up to 0.95. In general, the shorter issue text, possibly indicating precise issues, seems to improve the prediction accuracy with a strong negative correlation of $$-$$
-
0.73. We found that Relate-links often get confused with the other links, which suggests that they are likely used as default links in unclear cases. Our findings particularly on the quality and heterogeinity of issue link data have implications for researching and applying issue link prediction in practice.