Pathway Studio v.12 Release Notes
- 1. 1 1 Release Notes, Pathway Studio v12 September 2018 The v12 Release for Pathway Studio finalized the data structure and completed the support functionalities for Pathway Studio Ontology. The new Pathway Studio offers Cloud-hosted solutions for all workflows with improved content accessibility, advanced search capabilities and results sharing. New, highly relevant content was also added. The coverage of diseases, chemical and cellular effects in the Mammal and MammalPlus Knowledgebases were augmented with organ and tissue data. A new entity was added covering genetic variants extracted from the literature and imported from ClinVar with relations to genes and function. The Plant Knowledgebase was expanded with agriculture-relevant plant species. Finally, relevant drug-target relations from Reaxys Medicinal Chemistry are now integrated into and mapped to concepts in Pathway Studio. Five-Point Summary 1. Change font size and entity size for each individual entity: Modify the look of pathways to fit your presentation and publication needs. 2. Improved and expanded support of ontologies: a. Explore and search terms in Pathway Studio Ontology in a new Ontology Browser b. Right-click an entity and select Show in Ontology to look it up in the context of ontologies c. Use ontologies to add entities to pathways (e.g., add all inflammatory diseases) d. Use ontologies in experiment analysis (e.g., find all kinases). 3. Export improvements: Export entity properties (such as entity name and IDs) together with relation properties directly from the Relation Table View. 4. Share pathways and experiments in User Groups (for PSE only): Admins can set up User Groups for collaborating teams. Within a User Group you can: a. Copy a pathway, experiment or group to the Group Projects and allow other group members to modify your file. b. Copy a shortcut to your pathway, experiment or group to the Group Projects so other group members can see but not modify your file. 5. Content Enhancement: a. Enhanced anatomy data for insights at organ and tissue level b. Integration of drug-target relations from Reaxys Medicinal Chemistry c. A new entity centered on SNV/SNP genetic variation d. Expanded species coverage of the Plant Knowledgebase
- 2. 2 New Search Capabilities for Fast and Unparalleled Results Building on the new curated pathway data organization and structure introduced in v11.4, the v12 Release for Pathway Studio allows you to browse and view the context of specific entities within the hierarchical tree of the Pathway Studio Ontology. Thus, you can interpret search results within the context of the entity’s ontology to answer questions about the relevance of retrieved hits. You can also increase specificity of your search by quickly determining ontological terms that will produced the right results. Pathway Studio supports two ontologies: Gene Ontology (GO) for protein and gene names, and Pathway Studio Ontology, which supports all entities in the Knowledgebases — cell processes, clinical parameters, complexes, diseases, functional classes, proteins and gene names, small molecules and treatments. View an ontology by right-clicking the highlighted entity and selecting the GO or Pathway Studio Ontology. You can begin a focused search by first browsing the Pathway Studio Ontology (Fig. 1) to find terms aligned with your query. Alternatively, a broad search will return results from all ontology terms associated with the query, but with the update you can right-click any entity in the results table to view its location in the ontology and determine if the information is relevant to your query. The Pathway Studio Ontology is an underlying structure of Pathway Studio, so you can access it on entities in curated or user-defined pathways (Fig. 2), as well as on entities aligned to experimental results (Fig. 3) curated with Pathway Studio relationships. Fig. 1. Browse Pathway Studio Ontology to select objects and concepts of relevance to your search.
- 3. 3 Fig. 2. Use Pathway Studio Ontology to build pathways. Select Specific Ontology Categories in Network Builder and pick entities of interest. Fig. 3. Select the Ontological Categories tab to use ontologies in experiment analyses.
- 4. 4 Facilitated export of entity and relation properties An upgrade to the export functionality of Pathway Studio allows selecting entities and relation properties to be exported directly from the Relation Table View. Click Export and select Excel CSV/tab-delimited from the dropdown menu (Fig. 4). As output, you receive a single table with all selected properties. Fig. 4. Improved export functionality allows you to select entity and relation properties from the Relation Table View and export them together into a single table.
- 5. 5 Sharing Results in User Groups (available only in PSE) In response to customer feedback, Pathway Studio Web and Enterprise Cloud now enable creating User Groups to share results and projects with colleagues. Create one or more User Groups with different members and they appear listed under My Projects in Pathway Studio (Fig. 5). Shared results and pathways/networks are editable projects, which colleagues open and save. After editing, they can share the edits with the group. Fig. 5. Different paste options allow sharing pathways, results and experiments with colleagues in a User Group. Streamlined and improved Admin Functions (available only in PSE) Users with Admin rights can now manage Users and set up User Groups under the Admin menu. Furthermore, users with a Publisher role can easily submit pathways for approval and publication as user-generated pathways. Submitted pathways appear first in the Submissions tab visible to users with an Approver role and, once approved, become visible to everyone at the institution. The Submissions tab also accommodates approval and publication of experiments and User Groups. Content Enhancements Enhanced Anatomy data for Insights at Organ and Tissue Level The addition of 3,682 organs and tissues to the Pathway Studio Mammal and MammalPlus KnowledgeBases augments the number of relations that can be probed in Pathway Studio to >1.7 million. Tap into regulatory effects, gene expression, state changes and functional associations connecting cell processes, clinical parameters, diseases, compounds, and proteins to organs and tissues.
- 6. 6 Integration of Drug-Target Relations from Reaxys Medicinal Chemistry Reaxys Medicinal Chemistry (RMC) is a market-leading research system for bioactivity data. With over 20 million drug-target relations, RMC supports early drug discovery. Relevant relations (for human, mouse and rat) are now integrated and mapped to concepts in Pathway Studio, expanding the small molecules dataset to over 940,000 entities and delivering >1.1 million annotated relations for human, >32,000 for mouse and >140,000 for rat. Genetic Variant: a New SNV/SNP-Centered Entity A new database focusing on single-nucleotide variants (SNV) or single-nucleotide polymorphisms (SNP) adds another entity type to Pathway Studio and another dimension to explore the impact of genetic modifications on pathways and their functions. Data are extracted by MedScan from the scientific literature as well as imported from ClinVar, and have resulted to date in >330,000 entities, >130,000 relations by functional association (disease, clinical parameter, biological process), and >320,000 relations to genes. Expanded Plant Knowledgebase for Agricultural Biology Research To improve content for basic and applied agricultural research, the Pathway Studio Plant Knowledgebase has been expanded with seven model organisms. The models support research into gene functionality of the model and similar organisms. Select a specific model organism under Preferences. Organism Common name Description Brachypodium distachyon Stiff brome Closely related to and a model organism for wheat and barley. Populus trichocarpa California poplar A model organism for forestry research. Vitis vinifera Common grape A model organism for agricultural and viticultural research. Glycine max Soybean A model organism for crop research. Sorghum bicolor Sorghum A model organism for crop research. Solanum lycopersicum Tomato A model organism for crop and agricultural research. Fragaria vesca Woodland or wild strawberry A model for plants exhibiting multiploidy.