VariantEffect · bencap · Nov 19, 2025 · Nov 25, 2025 · Nov 25, 2025 · Nov 28, 2025
diff --git a/package-lock.json b/package-lock.json
diff --git a/package.json b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "mavedb-ui",
-  "version": "2025.5.2",
+  "version": "2026.1.0",
   "private": true,
   "type": "module",
   "scripts": {
@@ -15,6 +15,8 @@
     "@fortawesome/free-regular-svg-icons": "^7.0.0",
     "@fortawesome/free-solid-svg-icons": "^7.0.0",
     "@fortawesome/vue-fontawesome": "^3.1.1",
+    "@primevue/themes": "^4.4.1",
+    "@tailwindcss/vite": "^4.1.16",
     "@unhead/vue": "^2.0.17",
     "axios": "^1.11.0",
     "chart.js": "^4.4.1",
@@ -41,6 +43,8 @@
     "jsonpath-plus": "^10.3.0",
     "jsonwebtoken": "^9.0.2",
     "jszip": "^3.10.1",
+    "linkify-html": "^4.3.2",
+    "linkifyjs": "^4.3.2",
     "lodash": "^4.17.21",
     "marked": "^11.1.0",
     "moment": "^2.29.4",
@@ -52,12 +56,13 @@
     "pluralize": "^8.0.0",
     "primeflex": "^3.3.1",
     "primeicons": "^6.0.1",
-    "primevue": "3.52.0",
+    "primevue": "^4.4.1",
     "rest-client-vue": "^1.2.0-b2",
+    "tailwindcss": "^4.1.16",
     "universal-base64url": "~1.1.0",
     "uuid": "^9.0.1",
     "vee-validate": "^4.12.2",
-    "vue": "^3.3.11",
+    "vue": "^3.4.0",
     "vue-debounce": "^4.0.1",
     "vue-router": "^4.2.5",
     "vuex": "^4.1.0",

diff --git a/public/docs/mavedb/.buildinfo b/public/docs/mavedb/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: fe61ab4a9503c0d35fa0eb1b91172649
+config: ad4296d0777365c695d333cc4f10b8f1
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/public/docs/mavedb/_images/bard1_base_histogram.png b/public/docs/mavedb/_images/bard1_base_histogram.png
diff --git a/public/docs/mavedb/_images/bard1_clinical_histogram.png b/public/docs/mavedb/_images/bard1_clinical_histogram.png
diff --git a/public/docs/mavedb/_images/bard1_custom_histogram.png b/public/docs/mavedb/_images/bard1_custom_histogram.png
diff --git a/public/docs/mavedb/_images/bard1_protein_effect_histogram.png b/public/docs/mavedb/_images/bard1_protein_effect_histogram.png
diff --git a/public/docs/mavedb/_images/brca1_assay_facts_example.png b/public/docs/mavedb/_images/brca1_assay_facts_example.png
diff --git a/public/docs/mavedb/_images/msh2_heatmap.png b/public/docs/mavedb/_images/msh2_heatmap.png
diff --git a/public/docs/mavedb/_images/msh2_protein_structure.png b/public/docs/mavedb/_images/msh2_protein_structure.png
diff --git a/public/docs/mavedb/_sources/accession_numbers.rst.txt b/public/docs/mavedb/_sources/accession_numbers.rst.txt
@@ -1,12 +1,15 @@
 MaveDB accession numbers
 ============================
 
+.. _accession-numbers-intro:
+
 MaveDB accession numbers use the `URN (Uniform Resource Name) format <https://tools.ietf.org/html/rfc8141>`_.
 The accession numbers have a hierarchical structure that reflects the relationship between
-experiment sets, experiments, score sets, and individual variants in MaveDB.
+experiment sets, experiments, score sets, and individual variants in MaveDB. URNs are also used to uniquely identify
+other resources in MaveDB, such as calibrations and collections.
 
-All public accession numbers start with the string `urn:mavedb:` followed by the experiment set number
-(eight digits, zero-padded).
+URNs within the experiment set/experiment/score set/variant hierarchy start with the string `urn:mavedb:` 
+followed by the experiment set number (eight digits, zero-padded).
 Experiments are indexed by letter within the experiment set.
 If necessary, ``aa``, ``ab``, etc. will follow ``z``.
 Score sets are indexed by number within the experiment.
@@ -28,20 +31,42 @@ Score sets are indexed by number within the experiment.
    * - ``tmp:446191af-c1f8-4891-9f67-de152e9d328b``
      - temporary accession number
 
+.. _end-accession-numbers-intro:
+
 Meta-analysis accession numbers
 ####################################
 
+.. _meta-analysis-accession-numbers:
+
 Meta-analysis score sets use the special ``0`` experiment instead of a letter.
 
 Meta-analysis score sets that include data from a single experiment set will use that experiment set's number.
 For meta-analyses that use data from multiple experiment sets,
 a new experiment set number will be assigned for all meta-analyses that include data from the same experiment sets.
 These meta-analysis-only experiment sets will only contain the ``0`` experiment.
 
+.. _end-meta-analysis-accession-numbers:
+
 Temporary accession numbers
 ###################################
 
+.. _temporary-accession-numbers:
+
 When first uploaded, records are given a temporary accession number starting with ``tmp:``.
 These temporary accessions are not structured according to the record type.
 
 MaveDB URNs are created when the temporary records are made publicly viewable by publishing a score set.
+
+.. _end-temporary-accession-numbers:
+
+URNs for other resources
+###################################
+
+.. _other-resources-urns:
+
+Other resources in MaveDB that exists outside of the data set hierarchy, such as calibrations and collections, also use URNs starting with ``urn:mavedb:``.
+This is followed by a resource type identifier (e.g., ``calibration``, ``collection``) and a unique
+resource identifier. For example, the URN for a calibration resource might be
+``urn:mavedb:calibration-11111111-2222-3333-aaaa-bbbbccccdddd``.
+
+.. _end-other-resources-urns:
diff --git a/public/docs/mavedb/_sources/accounts.rst.txt b/public/docs/mavedb/_sources/accounts.rst.txt
@@ -1,28 +1,40 @@
 User account management
 ==================================
 
+.. _user-accounts-intro:
+
 User account authentication in MaveDB is handled through `ORCID iD <https://orcid.org/>`_.
 If you do not have an `ORCID iD <https://orcid.org/>`_, you can register a new one for free using their service.
 
 Your MaveDB account will be created once you log in for the first time.
 
+You must have logged in at least once to MaveDB using your ORCID iD in order to be added as a :ref:`contributor<data-set-contributors>` to a dataset.
+
+.. _end-user-accounts-intro:
+
 Setting an email address
 ###################################
 
+.. _setting-email-address:
+
 MaveDB can only view public email addresses associated with your `ORCID iD <https://orcid.org/>`_.
 If you do not have one of these set and would like to receive emails from MaveDB,
 you can provide an email address using the `Profile settings page <https://www.mavedb.org/#/settings/>`_
-(requires login).
+(requires login). To upload datasets, you must provide an email address.
 
-MaveDB will send automatic emails when upload tasks complete or when your dataset permissions are changed.
-MaveDB maintainers will also use this email address to notify you of important updates that affect the usability of
-your datasets.
+.. _end-setting-email-address:
 
 API access tokens
 ###################################
 
-Users can generate an API access token to access :ref:`private datasets<Temporary accession numbers>` via API
-using the `Profile settings page <https://www.mavedb.org/#/settings/>`_ (requires login).
+.. _api-access-tokens:
+
+Users may generate an API access token to authenticate with the `MaveDB API <https://api.mavedb.org/docs>`_. This token
+will allow you to perform actions such as uploading and modifying datasets programmatically, fetching :ref:`private data sets<temporary-accession-numbers>`, 
+or managing your account. You can generate and revoke API access tokens using the 
+`Profile settings page <https://www.mavedb.org/#/settings/>`_ (requires login). 
 
 Only one API access token can be active for a given account.
-Generating a new token will invalidate the old one.
+Generating a new token will invalidate the old one.
+
+.. _end-api-access-tokens:
diff --git a/public/docs/mavedb/_sources/api/index.rst.txt b/public/docs/mavedb/_sources/api/index.rst.txt
@@ -0,0 +1,10 @@
+MaveDB API
+==================================
+
+.. _mavedb-api-intro:
+
+The MaveDB API provides programmatic access to MaveDB data and functionality.
+
+You can explore the API documentation at the following link: `MaveDB API Documentation <https://api.mavedb.org/docs>`_.
+
+.. _end-mavedb-api-intro:
diff --git a/public/docs/mavedb/_sources/assay_facts.rst.txt b/public/docs/mavedb/_sources/assay_facts.rst.txt
@@ -0,0 +1,60 @@
+Assay facts
+===================================
+
+.. _assay-facts-intro:
+
+MaveDB captures key facts about the experimental assay used to generate variant effect measurements
+from controlled keywords based on a :ref:`controlled vocabulary<mave controlled vocabulary>`. This information is then used
+to generate a concise summary of assay facts that is displayed on the score set page.
+
+.. figure:: images/brca1_assay_facts_example.png
+   :name: assay-facts-example
+   :alt: Assay facts section from a MaveDB score set page
+   :align: left
+
+   Example of the assay facts section from a score set
+
+   This figure shows the assay facts section from 
+   `urn:mavedb:00000097-0-2 <https://mavedb.org/score-sets/urn:mavedb:00000097-0-2>`_,
+   which describes saturation genome editing of *BRCA1*.
+
+.. _end-assay-facts-intro:
+
+Assay fact sheet properties
+------------------------------------
+
+.. _assay-fact-sheet-properties:
+
+**Gene Symbol**
+    The HGNC gene symbol for the target gene being assayed.
+
+**Assay type**
+   The type of functional assay used to measure variant effects. This corresponds to the :ref:`phenotypic assay method<phenotypic assay method>` controlled vocabulary term.
+
+**Molecular mechanism**
+   The molecular mechanism by which the assay measures variant effects. This corresponds to the :ref:`molecular mechanism<molecular mechanism assessed>` controlled vocabulary term.
+
+**Variant consequences detected**
+    The types of variant consequences that the assay is capable of detecting. This corresponds to the :ref:`phenotypic assay mechanism<phenotypic assay mechanism>` controlled vocabulary term.
+
+**Model system**
+    The biological system in which the assay was performed. This corresponds to the :ref:`model system<phenotypic assay model system>` controlled vocabulary term.
+
+**Detects splicing variants**
+   Whether the assay is capable of detecting splicing variants. Based on assay design, and inferred based on a combination of the :ref:`variant library creation method<variant library creation methods>` and
+   other terms.
+
+**Detects nonsense-mediated decay (NMD) variants**
+   Whether the assay is capable of detecting NMD variants. Based on assay design, and inferred based on a combination of the :ref:`variant library creation method<variant library creation methods>` and
+   other terms.
+
+**OddsPaths**
+    The Odds of Pathogenicity score calculated for abnormal and normal functional readouts, if applicable. These OddsPaths are based on the framework described in `Brnich et al., 2019 <https://doi.org/10.1186/s13073-019-0690-2>`_.
+
+    .. note::
+       OddsPath calculations are provided when available. 
+
+       For some assays, MaveDB maintainers may have selected OddsPaths other than those submitted by the data contributor,
+       based on updated calibrations or reanalyses of the data. In these cases, the source of the OddsPath scores will be indicated on the score set page.
+
+.. _end-assay-fact-sheet-properties:
diff --git a/public/docs/mavedb/_sources/bulk_downloads.rst.txt b/public/docs/mavedb/_sources/bulk_downloads.rst.txt
@@ -0,0 +1,32 @@
+Bulk downloads
+==================================
+
+.. _bulk-downloads:
+
+A complete set of MaveDB data and metadata is available as a bulk download 
+hosted on `Zenodo <https://zenodo.org/>`_.
+
+.. note::
+   The associated DOI for the most recent version of the archive is
+   `10.5281/zenodo.11201736 <https://doi.org/10.5281/zenodo.11201736>`_.
+
+   The archive will be updated twice yearly in May and November.
+
+The archive contains a single JSON document called ``main.json`` that provides
+the structured metadata for every :ref:`experiment set<experiment sets>`,
+:ref:`experiment<experiments>`, and :ref:`score set<score sets>`.
+Score set data is provided in ``.csv`` format,
+with separate score and count files for each record as appropriate.
+Each file is named using the :ref:`score set urn<mavedb accession numbers>`.
+
+Users who are interested in downloading a large number of MaveDB datasets are
+strongly encouraged to use and cite these archival releases, 
+particularly for machine learning or AI-based studies where the associated data
+needs to be clearly identified for reproducibility.
+
+Datasets released using the `CC0 <https://creativecommons.org/public-domain/cc0/>`_
+public domain license are included in the archive, and this is the license
+applied to the archive itself.
+Datasets provided by MaveDB under other licenses are not currently included.
+
+.. _end-bulk-downloads:
diff --git a/public/docs/mavedb/_sources/citation.rst.txt b/public/docs/mavedb/_sources/citation.rst.txt
@@ -1,7 +1,21 @@
 Citing MaveDB
 ==================================
 
-When citing MaveDB, please refer to:
+.. _citing-mavedb:
+
+When citing MaveDB, please refer to the most recent publication:
+
+Rubin AF, Stone J, Bianchi AH, Capodanno BJ, Da EY, Dias M, Esposito D, 
+Frazer J, Fu Y, Grindstaff SB, Harrington MR, Li I, McEwen AE, Min JK, Moore N, 
+Moscatelli OG, Ong J, Polunina PV, Rollins JE, Rollins NJ, Snyder AE, 
+Tam A, Wakefield MJ, Ye SS, Starita LM, Bryant VL, Marks DS, Fowler DM. 
+MaveDB 2024: a curated community database with over seven million variant effects from multiplexed functional assays. 
+*Genome Biol.* 2025 Jan 21;26(1):13. 
+doi: `10.1186/s13059-025-03476-y <https://doi.org/10.1186/s13059-025-03476-y>`_.
+PMID: `39838450 <https://pubmed.ncbi.nlm.nih.gov/39838450/>`_;
+PMCID: `PMC11753097 <http://www.ncbi.nlm.nih.gov/pmc/articles/pmc11753097/>`_.
+
+The previous citation is:
 
 Esposito D, Weile J, Shendure J, Starita LM, Papenfuss AT, Roth FP, Fowler DM, Rubin AF.
 MaveDB: an open-source platform to distribute and interpret data from multiplexed assays of variant effect.
@@ -13,3 +27,5 @@ PMCID: `PMC6827219 <http://www.ncbi.nlm.nih.gov/pmc/articles/pmc6827219/>`_.
 When citing data downloaded from MaveDB, please refer to the MaveDB publication (above) as well as the original
 publications where the datasets were reported.
 These citations are usually available on the associated experiment and score set pages.
+
+.. _end-citing-mavedb:
diff --git a/public/docs/mavedb/_sources/clinical_view.rst.txt b/public/docs/mavedb/_sources/clinical_view.rst.txt