From eb0a504548e7ec47b89626402e23e33c4e9e6a59 Mon Sep 17 00:00:00 2001 From: ielis Date: Fri, 15 Nov 2024 10:55:09 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20monarch-?= =?UTF-8?q?initiative/gpsea@f71109f937e589896c1ec185c387221b2014be81=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .../_modules/gpsea/analysis/pscore/_hpo.html | 72 +++++++------------ .../user-guide/predicates/devries.rst.txt | 42 +++++++---- latest/searchindex.js | 2 +- latest/user-guide/predicates/devries.html | 53 +++++++++----- 4 files changed, 93 insertions(+), 76 deletions(-) diff --git a/latest/_modules/gpsea/analysis/pscore/_hpo.html b/latest/_modules/gpsea/analysis/pscore/_hpo.html index a8a4b4d0..ff3b46f6 100644 --- a/latest/_modules/gpsea/analysis/pscore/_hpo.html +++ b/latest/_modules/gpsea/analysis/pscore/_hpo.html @@ -255,7 +255,7 @@

Source code for gpsea.analysis.pscore._hpo

     ) -> float:
         """
         Calculate the dev delay component of the score
-        
+
         Args:
             observed_term_ids: terms observed in patient
 
@@ -266,32 +266,12 @@ 
Source code for gpsea.analysis.pscore._hpo
         for t in observed_term_ids:
             if t in self._gdd_tids:
                 return self._gdd_tids[t]
-        
+
         # Intellectual disability
         for t in observed_term_ids:
             if t in self._idd_tids:
                 return self._idd_tids[t]
-        
-        return 0
-
-    def _term_or_descendant(
-        self,
-        target_tid: str,
-        observed_term_ids: typing.Iterable[str],
-    ) -> int:
-        """
-        Args:
-            target_tid: term of interest
-            observed_term_ids: all terms observed in patient
 
-        Returns:
-            1 if the term or any descendant is present in the patient, otherwise 0
-        """
-        for term_id in observed_term_ids:
-            if term_id == target_tid \
-               or any(ancestor == target_tid for ancestor in self._hpo.graph.get_ancestors(term_id)):
-                return 1
-        
         return 0
 
     def _term_or_descendant_count(
@@ -305,14 +285,12 @@ 
Source code for gpsea.analysis.pscore._hpo
             observed_term_ids: all terms observed in patient
 
         Returns:
-            the total count of the terms equal to or descending from the target_tid
+            1 if at least one term is equal to or descending from the target_tid, otherwise 0
         """
-        total_count = 0
         for term_id in observed_term_ids:
-            for desc_tid in self._hpo.graph.get_ancestors(term_id, include_source=True):
-                if desc_tid.value == target_tid:
-                    total_count += 1
-        return total_count
+            if term_id == target_tid or self._hpo.graph.is_descendant_of(term_id, target_tid):
+                return 1
+        return 0
 
     def _postnatal_growth_score(
         self,
@@ -320,7 +298,7 @@ 
Source code for gpsea.analysis.pscore._hpo
     ) -> int:
         """
         Calculate the postnatal growth component of the score.
-        
+
         Args:
             observed_term_ids: terms observed in patient
 
@@ -332,7 +310,7 @@ 
Source code for gpsea.analysis.pscore._hpo
         tall_stature = 'HP:0000098'
         total_count = 0
         for tid in (microcephaly, short_stature, macrocephaly, tall_stature):
-            total_count += self._term_or_descendant(tid, observed_term_ids)
+            total_count += self._term_or_descendant_count(tid, observed_term_ids)
         if total_count > 2:
             raise ValueError(f"Inconsistent annotations for postnatal growth score {total_count}:  {observed_term_ids}")
         return total_count
@@ -353,14 +331,22 @@ 
Source code for gpsea.analysis.pscore._hpo
         Returns: facial dysmorphism score (between 0 and 2)
 
         """
-        hypertelorism = 'HP:0000316'
+        globe_location = 'HP:0100886'  # include Hypertelorism and others
+        lip = 'HP:0000159' # Abnormal lip morphology HP:0000159
         external_nose = 'HP:0010938'
         pinna_morphology = 'HP:0000377'
+        facial_shape = 'HP:0001999'  # Abnormal facial shape
+        midface = 'HP:0000309'  # Abnormal midface morphology
+        chin = 'HP:0000306'  # Abnormality of the chin
 
-        # No need to inspect descendants since Hypertelorism has none.
-        total_count = 1 if hypertelorism in observed_term_ids else 0
+        total_count = self._term_or_descendant_count(target_tid=globe_location, observed_term_ids=observed_term_ids)
+        total_count += self._term_or_descendant_count(target_tid=lip, observed_term_ids=observed_term_ids)
         total_count += self._term_or_descendant_count(target_tid=external_nose, observed_term_ids=observed_term_ids)
         total_count += self._term_or_descendant_count(target_tid=pinna_morphology, observed_term_ids=observed_term_ids)
+        total_count += self._term_or_descendant_count(target_tid=facial_shape, observed_term_ids=observed_term_ids)
+        total_count += self._term_or_descendant_count(target_tid=midface, observed_term_ids=observed_term_ids)
+        total_count += self._term_or_descendant_count(target_tid=chin, observed_term_ids=observed_term_ids)
+
         if total_count > 1:
             return 2
         else:
@@ -373,24 +359,20 @@ 
Source code for gpsea.analysis.pscore._hpo
         """
         Non-facial dysmorphism and congenital abnormalities component.
         One point is assigned for either the corresponding HPO terms or any of their descendents up to a maximum of 2.
-        
+
         Args:
             observed_term_ids:  terms observed in patient
 
         Returns:   Non-facial dysmorphism and congenital abnormalities score (between 0 and 2)
 
         """
-        hypospadias = 'HP:0000047'
+        abn_external_genitalia = 'HP:0000811'  # Abnormal external genitalia
         abnormal_hand_morphology = 'HP:0005922'
         abnormal_heart_morphology = 'HP:0001627'
-        # total_count = len([t for t in observed_term_ids if t == hypospadias])
-        total_count = self._term_or_descendant_count(
-            target_tid=hypospadias, observed_term_ids=observed_term_ids,
-        )
-        total_count += self._term_or_descendant_count(target_tid=abnormal_hand_morphology,
-                                                      observed_term_ids=observed_term_ids)
-        total_count += self._term_or_descendant_count(target_tid=abnormal_heart_morphology,
-                                                      observed_term_ids=observed_term_ids)
+
+        total_count = self._term_or_descendant_count(target_tid=abn_external_genitalia, observed_term_ids=observed_term_ids,)
+        total_count += self._term_or_descendant_count(target_tid=abnormal_hand_morphology, observed_term_ids=observed_term_ids)
+        total_count += self._term_or_descendant_count(target_tid=abnormal_heart_morphology, observed_term_ids=observed_term_ids)
         return min(2, total_count)
 
     def _prenatal_growth_score(
@@ -419,7 +401,7 @@ 
Source code for gpsea.analysis.pscore._hpo
     def score(self, patient: Patient) -> float:
         """
         Calculate score based on list of strings with term identifiers or observed HPO terms.
-        
+
         Args:
             patient: list of strings with term identifiers or observed HPO terms
 
@@ -433,7 +415,7 @@ 
Source code for gpsea.analysis.pscore._hpo
         facial_score = self._facial_dysmorphism_score(observed_term_ids)
         congen_score = self._congenital_score(observed_term_ids)
         prenatal_score = self._prenatal_growth_score(observed_term_ids)
-        
+
         return delay_score + growth_score + facial_score + congen_score + prenatal_score

 

 
diff --git a/latest/_sources/user-guide/predicates/devries.rst.txt b/latest/_sources/user-guide/predicates/devries.rst.txt
index 37989c86..84bbd948 100644
--- a/latest/_sources/user-guide/predicates/devries.rst.txt
+++ b/latest/_sources/user-guide/predicates/devries.rst.txt
@@ -15,7 +15,7 @@ Statistical significance of a difference in the De Vries score between groups ca
 determined using the Mann-Whitney-U test.
 
 We refer to `Feenstra et al. (2011) `_ for
-the original description of the adjusted De Vries score. Here we offer a version of the
+the original description of the adjusted De Vries score. Here we offer an adapted version of the
 score that leverages the structure of the Human Phenotype Ontology to assess the phenotype.
 
 
@@ -113,38 +113,54 @@ is 2 because the same individual cannot have both tall and short stature or both
 Facial dysmorphic features
 ~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-This section assigns two points if two or more anomalies are identified in the following
-categories: hypertelorism, nasal anomalies and ear anomalies. Our implementation of this feature counts the total
-number of terms or descendents of the following HPO terms.
+This section assigns two points if two or more facial dysmorphisms are identified. In contrast to the list of anomalies described
+in the original 2011 publication of the DeVries score, we leverage the structure of the HPO to include many more HPO terms that 
+denote various kinds of facial dysmorphism (e.g., `Abnormality of globe location `_ instead of just
+`Hypertelorism (HP:0000316) `_).
+
+Our implementation of this feature counts the total number of terms or descendents of the following HPO terms. Up to one point is given
+for each of the categories.
 
 +----------------------------------------------------------------------------------------------------------+-----------+
 | HPO term                                                                                                 | Score     |
 +==========================================================================================================+===========+
-| `Hypertelorism (HP:0000316) `_                               | 1         |
+| `Abnormality of globe location (HP:0000316) `_               | 0 or 1    |
++----------------------------------------------------------------------------------------------------------+-----------+
+| `Abnormal lip morphology (HP:0000159) `_                     |  0 or 1   |
++----------------------------------------------------------------------------------------------------------+-----------+
+| `Abnormal facial shape (HP:0001999) `_                       |  0 or 1   |
++----------------------------------------------------------------------------------------------------------+-----------+
+| `Abnormal midface morphology (HP:0000309) `_                 |  0 or 1   |
 +----------------------------------------------------------------------------------------------------------+-----------+
-| `Abnormal external nose morphology (HP:0010938) `_           | 1 each    |
+| `Abnormal forehead morphology (HP:0000290) `_                | 0 or 1    |
 +----------------------------------------------------------------------------------------------------------+-----------+
-| `Abnormal pinna morphology (HP:0000377)  `_                  | 1 each    |
+| `Abnormal chin morphology (HP:0000306) `_                    |  0 or 1   |
++----------------------------------------------------------------------------------------------------------+-----------+
+| `Abnormal external nose morphology (HP:0010938) `_           |  0 or 1   |
++----------------------------------------------------------------------------------------------------------+-----------+
+| `Abnormal pinna morphology (HP:0000377)  `_                  |  0 or 1   |
 +----------------------------------------------------------------------------------------------------------+-----------+
 
-If two or more terms are found, the score is 2, otherwise a score of zero is assigned.
+If items from two or more categories are found, the score is 2, otherwise a score of zero is assigned.
 
 
 Non-facial dysmorphism and congenital abnormalities
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-One point is assigned for either the
-corresponding HPO terms or any of their descendents up to a maximum of two points.
+One point is assigned for either the corresponding HPO terms or any of their descendents up to a maximum of two points.
+A maximum of one point is assigned for each of the following categories.
 
 +----------------------------------------------------------------------------------------------------------+-----------+
 | HPO term                                                                                                 | Score     |
 +==========================================================================================================+===========+
-| `Abnormal hand morphology (HP:0005922) `_                    | 1 each    |
+| `Abnormal hand morphology (HP:0005922) `_                    | 0 or 1    |
 +----------------------------------------------------------------------------------------------------------+-----------+
-| `Abnormal heart morphology (HP:0001627) `_                   | 1 each    |
+| `Abnormal heart morphology (HP:0001627) `_                   |  0 or 1   |
 +----------------------------------------------------------------------------------------------------------+-----------+
-| `Hypospadias (HP:0000047) `_                                 | 1         |
+| `Abnormal external genitalia morphology (HP:0000811) `_      |  0 or 1   |
 +----------------------------------------------------------------------------------------------------------+-----------+
 
+The score for this section can thus be 0, 1, or 2.
+
 
 Final score
 ~~~~~~~~~~~
diff --git a/latest/searchindex.js b/latest/searchindex.js
index 093a2bf6..f8e719a5 100644
--- a/latest/searchindex.js
+++ b/latest/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"alltitles": {"API reference": [[20, null]], "Alternative phenopacket sources": [[34, "alternative-phenopacket-sources"]], "Analysis": [[25, "analysis"], [26, "analysis"], [27, "analysis"], [28, "analysis"]], "Background": [[35, "background"]], "Biallelic predicate": [[44, "biallelic-predicate"]], "Biallelic predicate genotype groups": [[44, "id8"]], "Building blocks": [[45, "building-blocks"]], "Categories": [[44, "categories"]], "Change length of an allele": [[32, "change-length-of-an-allele"]], "Choose the transcript": [[34, "choose-the-transcript"]], "Choose the transcript and protein of interest": [[34, "choose-the-transcript-and-protein-of-interest"]], "Cohort exploratory analysis": [[30, null]], "Cohort summary": [[30, "cohort-summary"]], "Compare genotype and phenotype groups": [[26, null]], "Compare measurement values": [[25, null]], "Compare phenotype scores in genotype groups": [[27, null]], "Compare the individuals with EGFR mutation": [[36, "compare-the-individuals-with-egfr-mutation"]], "Compare the individuals with monoallelic and biallelic mutations": [[36, "compare-the-individuals-with-monoallelic-and-biallelic-mutations"]], "Complex conditions": [[45, "complex-conditions"]], "Configure a cohort creator": [[34, "configure-a-cohort-creator"]], "Configure analysis": [[25, "configure-analysis"], [26, "configure-analysis"], [27, "configure-analysis"], [28, "configure-analysis"]], "Contents:": [[24, null], [33, null], [39, null], [41, null], [42, null]], "Create a cohort from GA4GH phenopackets": [[34, "create-a-cohort-from-ga4gh-phenopackets"]], "Custom analysis": [[26, "custom-analysis"]], "De Vries Score": [[37, null]], "Default analysis": [[26, "default-analysis"]], "Developmental delay": [[37, "developmental-delay"]], "Distribution of variants across protein domains": [[30, "distribution-of-variants-across-protein-domains"]], "Enter features manually": [[34, "enter-features-manually"]], "Example": [[34, "example"], [34, "id4"], [40, "example"], [44, "example"], [44, "id5"], [44, "id6"]], "Example analysis": [[25, "example-analysis"], [26, "example-analysis"], [27, "example-analysis"], [28, "example-analysis"]], "Examples": [[36, "examples"]], "Exploration": [[30, "exploration"]], "Explore cohort": [[23, "explore-cohort"]], "Facial dysmorphic features": [[37, "facial-dysmorphic-features"]], "Feedback": [[21, "feedback"]], "Fetch data from UniProt REST API": [[34, "fetch-data-from-uniprot-rest-api"]], "Fetch protein data": [[34, "fetch-protein-data"]], "Fetch transcript coordinates from Variant Validator REST API": [[34, "fetch-transcript-coordinates-from-variant-validator-rest-api"]], "Final analysis": [[25, "final-analysis"], [27, "final-analysis"], [28, "final-analysis"]], "Final score": [[37, "final-score"]], "Fisher exact test (FET)": [[26, "fisher-exact-test-fet"]], "GPSEA": [[21, null]], "Gallery": [[41, "gallery"]], "General HPO terms": [[31, null]], "Genotype Predicates": [[39, null]], "Genotype phenotype associations": [[26, "genotype-phenotype-associations"]], "Genotype predicate": [[25, "genotype-predicate"], [26, "genotype-predicate"], [27, "genotype-predicate"], [28, "genotype-predicate"]], "Genotype-Phenotype Correlations in Autosomal Recessive Diseases": [[29, null]], "Get the transcript data": [[34, "get-the-transcript-data"]], "Glossary": [[32, null]], "Group by allele count": [[36, null]], "Group by diagnosis": [[38, null]], "Group by sex": [[43, null]], "Group by variant category": [[44, null]], "HMF01 - Skip terms that occur very rarely": [[35, "hmf01-skip-terms-that-occur-very-rarely"]], "HMF02 - Skip terms if no genotype group has more than one count": [[35, "hmf02-skip-terms-if-no-genotype-group-has-more-than-one-count"]], "HMF03 - Skip terms if all counts are identical to counts for a child term": [[35, "hmf03-skip-terms-if-all-counts-are-identical-to-counts-for-a-child-term"]], "HMF05 - Skip term if one of the genotype groups has neither observed nor excluded observations": [[35, "hmf05-skip-term-if-one-of-the-genotype-groups-has-neither-observed-nor-excluded-observations"]], "HMF06 - Skip term if underpowered for 2x2 or 2x3 analysis": [[35, "hmf06-skip-term-if-underpowered-for-2x2-or-2x3-analysis"]], "HMF07 - Skipping terms that are not descendents of Phenotypic abnormality": [[35, "hmf07-skipping-terms-that-are-not-descendents-of-phenotypic-abnormality"]], "HMF08 - Skipping \u201cgeneral\u201d level terms": [[35, "hmf08-skipping-general-level-terms"]], "HMF09 - Skipping terms that are rare on the cohort level": [[35, "hmf09-skipping-terms-that-are-rare-on-the-cohort-level"]], "HPO MT filter strategy": [[35, "hpo-mt-filter-strategy"]], "HPO predicate": [[40, null]], "Implementation in GPSEA": [[35, "implementation-in-gpsea"]], "Input data": [[34, null]], "Installation": [[22, null]], "Interactive exploration": [[30, "interactive-exploration"]], "Inverting conditions": [[45, "inverting-conditions"]], "Kaplan-Meier curves": [[28, "kaplan-meier-curves"]], "Latest release": [[22, "latest-release"]], "Length of the reference allele": [[32, "length-of-the-reference-allele"]], "Literature": [[21, "literature"]], "Load HPO": [[23, "load-hpo"], [27, "load-hpo"]], "Load cohort": [[25, "load-cohort"], [26, "load-cohort"], [27, "load-cohort"], [28, "load-cohort"], [45, "load-cohort"]], "Load phenopackets": [[34, "load-phenopackets"]], "MT filters: Choosing which terms to test": [[35, "mt-filters-choosing-which-terms-to-test"]], "Mann-Whitney U Test": [[27, "mann-whitney-u-test"]], "Monoallelic predicate": [[44, "monoallelic-predicate"]], "Monoallelic predicate genotype groups": [[44, "id7"]], "Multiple-testing correction": [[35, null]], "Multiple-testing correction procedures": [[35, "multiple-testing-correction-procedures"]], "Need more?": [[41, "need-more"]], "Non-facial dysmorphism and congenital abnormalities": [[37, "non-facial-dysmorphism-and-congenital-abnormalities"]], "Parse UniProt JSON dump": [[34, "parse-uniprot-json-dump"]], "Partitions": [[44, "partitions"]], "Persist the cohort for later": [[34, "persist-the-cohort-for-later"]], "Phenotype Predicates": [[42, null]], "Phenotype predicates": [[26, "phenotype-predicates"]], "Phenotype score": [[25, "phenotype-score"], [27, "phenotype-score"]], "Plot distribution of cohort variants on the protein": [[34, "plot-distribution-of-cohort-variants-on-the-protein"]], "Plot distribution of variants with respect to the protein sequence": [[23, "plot-distribution-of-variants-with-respect-to-the-protein-sequence"], [30, "plot-distribution-of-variants-with-respect-to-the-protein-sequence"]], "Postnatal growth abnormalities": [[37, "postnatal-growth-abnormalities"]], "Power": [[30, "power"]], "Predicates": [[41, null]], "Predicates for all cohort phenotypes": [[40, "predicates-for-all-cohort-phenotypes"]], "Prenatal-onset growth retardation": [[37, "prenatal-onset-growth-retardation"]], "Prepare cohort": [[23, "prepare-cohort"]], "Prepare 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\ No newline at end of file
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"umod": 28, "unambigu": 38, "unavail": 15, "under": [17, 23, 34, 35], "underli": 45, "undoubtedli": 34, "uniform": 6, "uninterest": 31, "uniprot": [15, 17, 30], "uniprot_json": [15, 34], "uniprotproteinmetadataservic": [0, 15, 17], "uniqu": [2, 3, 15, 23, 30], "unit": [15, 16, 22, 30], "unknown": [6, 15, 23, 30], "unknown_sex": [15, 43], "unless": [7, 23, 34, 35, 40], "unlik": [31, 35], "unnecessari": 31, "unsur": 30, "until": [11, 28], "untransl": [15, 34], "up": [23, 27, 35, 37, 40], "upper": [23, 26, 31], "upstream": 16, "upstream_gene_vari": [15, 17], "urat": 31, "uri": 15, "urin": 31, "urinari": 31, "urobilinogen": 31, "us": [1, 2, 3, 6, 7, 8, 10, 11, 13, 14, 15, 16, 17, 18, 19, 21, 23, 25, 26, 27, 28, 30, 32, 34, 35, 36, 39, 40, 41, 44, 45], "usabl": [1, 3], "usag": [6, 7, 9, 19, 45], "use_al": 35, "usealltermsmtcfilt": [1, 2, 35], "user": [15, 19, 21, 23, 26, 30, 31, 34], "usual": [6, 15, 26, 31, 41], "utf": [17, 18], "util": [0, 6, 26], "utr": [15, 34], "uvea": 31, "v": [21, 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"variantcoordin": [0, 15, 17, 32], "variantcoordinatefind": [0, 17], "varianteffect": [0, 6, 15, 17, 19, 23, 25, 26, 27, 44, 45], "variantformatt": [0, 19], "variantinfo": [0, 15], "variantinfoawar": [0, 15], "variantpred": [5, 6, 23, 25, 26, 27, 28, 36, 39, 41, 44, 45], "varianttranscriptproteinartist": 19, "varianttranscriptvisu": [0, 19], "variou": [16, 37], "vascular": 31, "vasculatur": 31, "vc": [15, 17], "vcf": 15, "vcv000522858": 45, "ventricular": [23, 26, 30, 31, 32], "vep": 17, "vepfunctionalannot": [0, 17], "veri": [2, 44], "verify_term_id": 2, "version": [4, 23, 26, 27, 37, 40], "versu": 28, "vessel": 31, "via": [7, 14, 17, 19, 34], "view": [0, 21, 23, 26, 30, 34], "viewer": [23, 30], "virtual": 22, "vision": 31, "visual": [19, 23, 27, 30, 31, 34], "vital": [11, 15], "vital_statu": 15, "vitalstatu": [0, 15], "vitamin": 31, "voic": 31, "vol": 15, "volum": [8, 15, 25, 27, 31], "vri": [8, 33, 42], "vvhgvsvariantcoordinatefind": [0, 17], "vvmulticoordinateservic": [0, 17, 23, 30, 34], "w": [15, 17], "wa": [1, 2, 3, 5, 7, 15, 19, 23, 25, 26, 27, 28, 30, 35, 37, 40, 45], "wai": [23, 24, 30, 34], "waist": 31, "wall": 31, "want": [2, 8, 26, 27, 34, 35, 36, 44, 45], "warn": [17, 23, 34], "we": [2, 3, 6, 8, 11, 15, 17, 18, 19, 21, 22, 23, 25, 26, 27, 28, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45], "websit": 34, "week": 15, "weight": 31, "well": [6, 7, 15, 30, 34, 38], "were": [1, 3, 17, 19, 23, 26, 27, 30, 34, 40], "what": [26, 39], "whatsoev": 6, "when": [2, 7, 15, 28, 34, 35, 40], "where": [1, 2, 3, 15, 17, 23, 37, 44], "wherea": 30, "whether": [7, 8, 15, 21, 26, 30], "which": [1, 2, 4, 5, 7, 15, 23, 26, 30, 33, 34, 37, 44, 45], "while": [4, 15, 26, 29, 36, 41, 44], "whisker": 27, "whitnei": [8, 9, 24, 30, 33, 37, 42], "who": [7, 23, 27, 29, 44], "whose": [15, 23, 26, 27, 40], "why": 2, "widespread": 30, "wikipedia": 30, "wilcoxon": 27, "wise": [23, 35], "with_cache_fold": 17, "with_strand": 16, "within": [15, 23, 26, 27, 30], "without": [6, 11, 26, 30], "word": [21, 31], "wordsmith": 25, "work": [2, 13, 17, 26, 34], "workflow": 30, "worth": 2, "would": [2, 8, 15, 21, 26, 27, 29, 30, 35, 37, 45], "wrap": [8, 15, 26, 34, 45], "wrap_scoring_funct": 8, "wrapper": [4, 9, 12, 18], "write": [17, 18, 19], "written": 19, "wwox": 40, "x": [27, 28], "x_1000001_1000027_": 15, "x_1000001_1000027_taaaaaaaaaaaaaaaaaaaaaaaaaa_t": 15, "x_12345_12345_c_g": [6, 15], "xaxi": 28, "xlabel": 28, "xm_": 17, "xu": 25, "y": [15, 27, 28], "ye": [1, 3, 7, 40], "year": [15, 17, 28], "yet": 15, "yield": 35, "ylabel": [27, 28], "ylim": 27, "you": [14, 15, 16, 30, 34, 35], "your": [16, 22, 34], "zero": [2, 6, 16, 32, 36, 37], "zero_vs_on": 6, "zero_vs_one_vs_two": 6, "zinc": 15, "zinc_fing": 15, "\u03b1": 15, "\u03c72": 4}, "titles": ["gpsea package", "gpsea.analysis package", "gpsea.analysis.mtc_filter package", "gpsea.analysis.pcats package", "gpsea.analysis.pcats.stats package", "gpsea.analysis.predicate package", "gpsea.analysis.predicate.genotype package", "gpsea.analysis.predicate.phenotype package", "gpsea.analysis.pscore package", "gpsea.analysis.pscore.stats package", "gpsea.analysis.temporal package", "gpsea.analysis.temporal.endpoint package", "gpsea.analysis.temporal.stats package", "gpsea.config module", "gpsea.io module", "gpsea.model package", "gpsea.model.genome package", "gpsea.preprocessing package", "gpsea.util module", "gpsea.view package", "API reference", "GPSEA", "Installation", "Tutorial", "Statistical analyses", "Compare measurement values", "Compare genotype and phenotype groups", "Compare phenotype scores in genotype groups", "Survival analysis", "Genotype-Phenotype Correlations in Autosomal Recessive Diseases", "Cohort exploratory analysis", "General HPO terms", "Glossary", "User guide", "Input data", "Multiple-testing correction", "Group by allele count", "De Vries Score", "Group by diagnosis", "Genotype Predicates", "HPO predicate", "Predicates", "Phenotype Predicates", "Group by sex", "Group by variant category", "Variant Predicates"], "titleterms": {"2x2": 35, "2x3": 35, "The": [23, 37], "abnorm": [35, 37], "across": 30, "all": [23, 35, 40], "allel": [23, 32, 36], "altern": 34, "an": 32, "analys": 24, "analysi": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 23, 25, 26, 27, 28, 30, 35], "api": [20, 34], "ar": 35, "associ": 26, "autosom": 29, "background": 35, "biallel": [36, 44], "block": 45, "build": 45, "categori": 44, "chang": 32, "child": 35, "choos": [34, 35], "code": 37, "cohort": [23, 25, 26, 27, 28, 30, 34, 35, 40, 45], "compar": [25, 26, 27, 36], "complex": 45, "condit": 45, "config": 13, "configur": [25, 26, 27, 28, 34], "congenit": 37, "content": [24, 33, 39, 41, 42], "control": 34, "coordin": 34, "correct": 35, "correl": 29, "count": [35, 36], "creat": 34, "creator": 34, "curv": 28, "custom": 26, "data": [28, 34], "de": 37, "default": 26, "delai": 37, "descend": 35, "development": 37, "diagnosi": 38, "diseas": 29, "distribut": [23, 30, 34], "domain": 30, "dump": 34, "dysmorph": 37, "egfr": 36, "endpoint": [11, 28], "enter": 34, "exact": 26, "exampl": [25, 26, 27, 28, 34, 36, 40, 44], "exclud": 35, "explor": [23, 30], "exploratori": 30, "facial": 37, "featur": [34, 37], "feedback": 21, "fet": 26, "fetch": 34, "filter": 35, "final": [25, 27, 28, 37], "fisher": 26, "frameshift": [23, 26], "from": 34, "ga4gh": 34, "galleri": 41, "gener": [31, 35], "genom": 16, "genotyp": [6, 23, 25, 26, 27, 28, 29, 34, 35, 39, 44], "get": 34, "glossari": 32, "gpsea": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 35], "group": [26, 27, 35, 36, 38, 43, 44], "growth": 37, "guid": 33, "ha": 35, "hmf01": 35, "hmf02": 35, "hmf03": 35, "hmf05": 35, "hmf06": 35, "hmf07": 35, "hmf08": 35, "hmf09": 35, "hpo": [23, 27, 31, 35, 40], "ident": 35, "implement": 35, "individu": 36, "input": 34, "instal": 22, "interact": 30, "interest": 34, "invert": 45, "io": 14, "json": 34, "kaplan": 28, "later": 34, "latest": 22, "length": 32, "level": 35, "literatur": 21, "load": [23, 25, 26, 27, 28, 34, 45], "mann": 27, "manual": 34, "measur": 25, "meier": 28, "missens": 23, "missing_implies_phenotype_exclud": 40, "model": [15, 16], "modul": [13, 14, 18], "monoallel": [36, 44], "more": [35, 41], "mt": 35, "mtc_filter": 2, "multipl": 35, "mutat": 36, "need": 41, "neither": 35, "non": 37, "nor": 35, "observ": 35, "occur": 35, "one": 35, "onset": 37, "packag": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 15, 16, 17, 19], "pars": 34, "partit": 44, "path": 32, "pcat": [3, 4], "persist": 34, "phenopacket": 34, "phenotyp": [7, 23, 25, 26, 27, 29, 34, 35, 40, 42], "plot": [23, 30, 34], "postnat": 37, "power": 30, "predic": [5, 6, 7, 23, 25, 26, 27, 28, 39, 40, 41, 42, 44, 45], "prenat": 37, "prepar": 23, "preprocess": 17, "procedur": 35, "protein": [23, 30, 34], "provid": 34, "pscore": [8, 9], "qualiti": 34, "rare": 35, "raw": 28, "recess": 29, "refer": [20, 32], "releas": 22, "respect": [23, 30], "rest": [26, 34], "retard": 37, "rule": 32, "run": 22, "score": [25, 27, 37], "scorer": 37, "section": 37, "sequenc": [23, 30], "sex": 43, "shape": 4, "show": 23, "showcas": 34, "skip": 35, "sourc": 34, "specifi": 35, "stabl": 22, "standard": 34, "stat": [4, 9, 12], "statist": [24, 25, 26, 27, 28, 30], "strategi": 35, "submodul": 0, "subpackag": [0, 1, 3, 5, 8, 10, 15], "summar": 23, "summari": [23, 30], "support": 4, "surviv": 28, "tbx5": [23, 26], "tempor": [10, 11, 12], "term": [31, 35], "test": [22, 25, 26, 27, 28, 30, 35], "than": 35, "transcript": 34, "true": 32, "tutori": [23, 29], "type": 30, "u": 27, "underpow": 35, "uniprot": 34, "us": 37, "user": 33, "util": 18, "v": [23, 26], "valid": 34, "valu": 25, "variant": [23, 30, 34, 44, 45], "veri": 35, "view": 19, "vri": 37, "which": 35, "whitnei": 27}})
\ No newline at end of file
diff --git a/latest/user-guide/predicates/devries.html b/latest/user-guide/predicates/devries.html
index da1716e9..e9b8826b 100644
--- a/latest/user-guide/predicates/devries.html
+++ b/latest/user-guide/predicates/devries.html
@@ -112,7 +112,7 @@
 Statistical significance of a difference in the De Vries score between groups can be
 determined using the Mann-Whitney-U test.

 
We refer to Feenstra et al. (2011) for
-the original description of the adjusted De Vries score. Here we offer a version of the
+the original description of the adjusted De Vries score. Here we offer an adapted version of the
 score that leverages the structure of the Human Phenotype Ontology to assess the phenotype.

 

 
The sections of the score

@@ -230,9 +230,12 @@ 
Postnatal growth abnormalities
 
Facial dysmorphic features

-
This section assigns two points if two or more anomalies are identified in the following
-categories: hypertelorism, nasal anomalies and ear anomalies. Our implementation of this feature counts the total
-number of terms or descendents of the following HPO terms.

+
This section assigns two points if two or more facial dysmorphisms are identified. In contrast to the list of anomalies described
+in the original 2011 publication of the DeVries score, we leverage the structure of the HPO to include many more HPO terms that
+denote various kinds of facial dysmorphism (e.g., Abnormality of globe location instead of just
+Hypertelorism (HP:0000316)).

+
Our implementation of this feature counts the total number of terms or descendents of the following HPO terms. Up to one point is given
+for each of the categories.

 
@@ -240,23 +243,38 @@ 
Facial dysmorphic features

-
+
+
+
+
+
+
+
+
+
+
+
-
-
+
+
-
-
+
+
+
+
+
+
+
+

 
 
HPO term
Hypertelorism (HP:0000316)
1
Abnormality of globe location (HP:0000316)
0 or 1
Abnormal lip morphology (HP:0000159)
0 or 1
Abnormal facial shape (HP:0001999)
0 or 1
Abnormal midface morphology (HP:0000309)
0 or 1

 
Abnormal external nose morphology (HP:0010938)
1 each
Abnormal forehead morphology (HP:0000290)
0 or 1

 
Abnormal pinna morphology (HP:0000377)
1 each
Abnormal chin morphology (HP:0000306)
0 or 1
Abnormal external nose morphology (HP:0010938)
0 or 1
Abnormal pinna morphology (HP:0000377)
0 or 1

 

 
 

-
If two or more terms are found, the score is 2, otherwise a score of zero is assigned.

+
If items from two or more categories are found, the score is 2, otherwise a score of zero is assigned.

 

 

 
Non-facial dysmorphism and congenital abnormalities

-
One point is assigned for either the
-corresponding HPO terms or any of their descendents up to a maximum of two points.

+
One point is assigned for either the corresponding HPO terms or any of their descendents up to a maximum of two points.
+A maximum of one point is assigned for each of the following categories.

 
@@ -265,16 +283,17 @@ 
Non-facial dysmorphism and congenital abnormalities
 

-
+
-
+
-
-
+
+

 
 
HPO term

 
Abnormal hand morphology (HP:0005922)
1 each
0 or 1

 

 
Abnormal heart morphology (HP:0001627)
1 each
0 or 1

 
Hypospadias (HP:0000047)
1
Abnormal external genitalia morphology (HP:0000811)
0 or 1

 

 
 

+
The score for this section can thus be 0, 1, or 2.

 

 

 
Final score