We present semantic-pragmatic specification and annotation (ellipsis, coreference, bridging and discourse relations, information structure, scope of negation) in the multi-layer, genre-diversified, 3+ million-token Prague Dependency Treebank – Consolidated 2. 0. While morphology and syntax work almost exclusively on sentence level, the semantic-pragmatic phenomena are often related to two or more neighbouring sentences and possibly to an extra-linguistic context. In the contribution, we describe these phenomena from both the linguistic perspective (form of expression, relation to syntax and morphology) and the cognitive perspective (relation to context, real world knowledge, as well as to the related processes such as thinking or reasoning) – classifying the possible relations between the semantic-pragmatic units into cognitively plausible, distinguishable, and human-understandable categories. We have applied our results to the corpus, by annotating it in its entirety. The resulting dataset is publicly and freely available, to serve for verification and further investigation of (not only) these phenomena.