diff --git a/src/codecs/jats/__file_snapshots__/06908fc3-73df-1014-bb56-a21daa237ef0.json b/src/codecs/jats/__file_snapshots__/06908fc3-73df-1014-bb56-a21daa237ef0.json
index e1e800d03..d881ea539 100644
--- a/src/codecs/jats/__file_snapshots__/06908fc3-73df-1014-bb56-a21daa237ef0.json
+++ b/src/codecs/jats/__file_snapshots__/06908fc3-73df-1014-bb56-a21daa237ef0.json
@@ -1595,6 +1595,10 @@
"type": "Date",
"value": "2015"
},
+ "isPartOf": {
+ "type": "Periodical",
+ "name": "Nature"
+ },
"title": "Non-adaptive plasticity potentiates rapid adaptive evolution of gene expression in nature"
},
{
@@ -2552,6 +2556,10 @@
"type": "Date",
"value": "2021"
},
+ "isPartOf": {
+ "type": "Periodical",
+ "name": "R package version 1.7.1-1"
+ },
"title": "emmeans: Estimated Marginal Means, aka Least-Squares Means"
},
{
@@ -2714,6 +2722,10 @@
"value": "XXXX"
}
],
+ "isPartOf": {
+ "type": "Periodical",
+ "name": "bioRxiv"
+ },
"title": "Variation in mutational (co)variances"
},
{
@@ -2780,6 +2792,10 @@
"type": "Date",
"value": "2019"
},
+ "isPartOf": {
+ "type": "Periodical",
+ "name": "bioRxiv"
+ },
"pageStart": 778282,
"title": "Phenotypic stasis with genetic divergence"
},
@@ -3731,6 +3747,10 @@
"value": "10.1101/506865"
}
],
+ "isPartOf": {
+ "type": "Periodical",
+ "name": "Ecology Letters, page"
+ },
"title": "How differing modes of non-genetic inheritance affect population viability in fluctuating environments"
},
{
@@ -4114,6 +4134,10 @@
"type": "Date",
"value": "2018"
},
+ "isPartOf": {
+ "type": "Periodical",
+ "name": "R package version 2.18.2"
+ },
"title": "RStan: the R interface to Stan"
},
{
diff --git a/src/codecs/jats/__file_snapshots__/48c60452-6c66-1014-adf9-c7b61873ecd3.json b/src/codecs/jats/__file_snapshots__/48c60452-6c66-1014-adf9-c7b61873ecd3.json
index cc71eb354..628e9fbb0 100644
--- a/src/codecs/jats/__file_snapshots__/48c60452-6c66-1014-adf9-c7b61873ecd3.json
+++ b/src/codecs/jats/__file_snapshots__/48c60452-6c66-1014-adf9-c7b61873ecd3.json
@@ -255,6 +255,10 @@
"type": "Date",
"value": "2022"
},
+ "isPartOf": {
+ "type": "Periodical",
+ "name": "Circular Statistics (version 0.4-94)"
+ },
"title": "R package “circular”"
},
{
@@ -1934,6 +1938,10 @@
"value": "10.1093/jxb/51.349.1403"
}
],
+ "isPartOf": {
+ "type": "Periodical",
+ "name": "J Exp Bot"
+ },
"title": "Hormonal influence on photocontrol of the protandry in the genus Helianthus"
},
{
@@ -2851,7 +2859,7 @@
"value": "10.3120/0024-9637-56.3.209"
}
],
- "title": "Patterson B. 2009. Systematics, Evolution, and Biogeography of Compositae, Madroño. doi:10.3120/0024-9637-56.3.209"
+ "title": "Systematics, Evolution, and Biogeography of Compositae, Madroño"
},
{
"type": "Article",
diff --git a/src/codecs/jats/__file_snapshots__/8758d58a-6c3d-1014-87a3-bbc202f7d832.json b/src/codecs/jats/__file_snapshots__/8758d58a-6c3d-1014-87a3-bbc202f7d832.json
index c596121db..122e05f75 100644
--- a/src/codecs/jats/__file_snapshots__/8758d58a-6c3d-1014-87a3-bbc202f7d832.json
+++ b/src/codecs/jats/__file_snapshots__/8758d58a-6c3d-1014-87a3-bbc202f7d832.json
@@ -1103,6 +1103,10 @@
"type": "Date",
"value": "1988"
},
+ "isPartOf": {
+ "type": "PublicationVolume",
+ "volumeNumber": 8
+ },
"title": "T-cell antigen receptor genes and T-cell recognition",
"meta": {
"label": "9."
@@ -5685,11 +5689,7 @@
"value": "10.1146/annurev-immunol-102819-023144"
}
],
- "isPartOf": {
- "type": "Periodical",
- "name": "Annu. Rev. Immunol."
- },
- "title": "A. C. Hayday, P. Vantourout, Annu. Rev. Immunol., in press, doi:10.1146/annurev-immunol-102819-023144.",
+ "title": "Annu. Rev. Immunol.",
"meta": {
"label": "46."
}
@@ -6651,6 +6651,10 @@
]
}
],
+ "isPartOf": {
+ "type": "PublicationVolume",
+ "volumeNumber": 8
+ },
"title": "OLGA: fast computation of generation probabilities of B- and T-cell receptor amino acid sequences and motifs",
"meta": {
"label": "62."
diff --git a/src/codecs/jats/__file_snapshots__/ca7917ff-6cb0-1014-9b19-d05ef1e56b05.json b/src/codecs/jats/__file_snapshots__/ca7917ff-6cb0-1014-9b19-d05ef1e56b05.json
index 4c372b6ba..7bbcc7393 100644
--- a/src/codecs/jats/__file_snapshots__/ca7917ff-6cb0-1014-9b19-d05ef1e56b05.json
+++ b/src/codecs/jats/__file_snapshots__/ca7917ff-6cb0-1014-9b19-d05ef1e56b05.json
@@ -3538,13 +3538,9 @@
},
"isPartOf": {
"type": "PublicationVolume",
- "isPartOf": {
- "type": "Periodical",
- "name": "Internal amino acid state modulates yeast taste neurons to support protein homeostasis in Drosophila"
- },
"volumeNumber": 29
},
- "title": "Steck K, Walker SJ, Itskov PM, Baltazar C, Moreira J-M, Ribeiro C. 2018. Internal amino acid state modulates yeast taste neurons to support protein homeostasis in Drosophila 29."
+ "title": "Internal amino acid state modulates yeast taste neurons to support protein homeostasis in Drosophila"
},
{
"type": "Article",
diff --git a/src/codecs/jats/__file_snapshots__/d6f14042-6db3-1014-b228-f9da7cb8e4cc.json b/src/codecs/jats/__file_snapshots__/d6f14042-6db3-1014-b228-f9da7cb8e4cc.json
index 3b38811c7..607d61dbf 100644
--- a/src/codecs/jats/__file_snapshots__/d6f14042-6db3-1014-b228-f9da7cb8e4cc.json
+++ b/src/codecs/jats/__file_snapshots__/d6f14042-6db3-1014-b228-f9da7cb8e4cc.json
@@ -1466,6 +1466,10 @@
"type": "Date",
"value": "2021"
},
+ "isPartOf": {
+ "type": "Periodical",
+ "name": "MedRxiv"
+ },
"title": "Obesity and accelerated epigenetic aging in a high-risk cohort of children",
"url": "https://doi.org/10.1101/2021.11.03.21265865"
},
@@ -3091,6 +3095,10 @@
"type": "Date",
"value": "2021"
},
+ "isPartOf": {
+ "type": "Periodical",
+ "name": "MedRxiv"
+ },
"title": "BMI is positively associated with accelerated epigenetic aging in twin pairs discordant for BMI",
"url": "https://doi.org/10.1101/2021.03.11.21253271"
},
diff --git a/src/codecs/jats/__file_snapshots__/e9291f49-6d06-1014-9500-e156797df82e.json b/src/codecs/jats/__file_snapshots__/e9291f49-6d06-1014-9500-e156797df82e.json
index b36252fe7..6a08ca6f3 100644
--- a/src/codecs/jats/__file_snapshots__/e9291f49-6d06-1014-9500-e156797df82e.json
+++ b/src/codecs/jats/__file_snapshots__/e9291f49-6d06-1014-9500-e156797df82e.json
@@ -574,7 +574,7 @@
"type": "Date",
"value": "2010"
},
- "title": "Andrews, S., 2010. FastQC: a quality control tool for high throughput sequence data."
+ "title": "FastQC: a quality control tool for high throughput sequence data"
},
{
"type": "Article",
diff --git a/src/codecs/jats/__file_snapshots__/elife-30274-v1.jats.xml b/src/codecs/jats/__file_snapshots__/elife-30274-v1.jats.xml
index deafe3e7c..499ab430c 100644
--- a/src/codecs/jats/__file_snapshots__/elife-30274-v1.jats.xml
+++ b/src/codecs/jats/__file_snapshots__/elife-30274-v1.jats.xml
@@ -1920,6 +1920,7 @@
R: A language and environment for statistical computing
2017
+
[
diff --git a/src/codecs/jats/__file_snapshots__/elife-30274-v1.yaml b/src/codecs/jats/__file_snapshots__/elife-30274-v1.yaml
index 366b22533..b2e3947df 100644
--- a/src/codecs/jats/__file_snapshots__/elife-30274-v1.yaml
+++ b/src/codecs/jats/__file_snapshots__/elife-30274-v1.yaml
@@ -1837,6 +1837,9 @@ references:
datePublished:
type: Date
value: '2017'
+ isPartOf:
+ type: Periodical
+ name: R Foundation for Statistical Computing
title: 'R: A language and environment for statistical computing'
- type: Article
id: bib26
diff --git a/src/codecs/jats/__file_snapshots__/elife-43154-v2.jats.xml b/src/codecs/jats/__file_snapshots__/elife-43154-v2.jats.xml
index a4833f930..89acf716a 100644
--- a/src/codecs/jats/__file_snapshots__/elife-43154-v2.jats.xml
+++ b/src/codecs/jats/__file_snapshots__/elife-43154-v2.jats.xml
@@ -1573,6 +1573,7 @@
2019
+
]
[
diff --git a/src/codecs/jats/__file_snapshots__/elife-43154-v2.yaml b/src/codecs/jats/__file_snapshots__/elife-43154-v2.yaml
index 69f54018b..f08dbda90 100644
--- a/src/codecs/jats/__file_snapshots__/elife-43154-v2.yaml
+++ b/src/codecs/jats/__file_snapshots__/elife-43154-v2.yaml
@@ -1281,6 +1281,9 @@ references:
datePublished:
type: Date
value: '2019'
+ isPartOf:
+ type: Periodical
+ name: GitHub
title: Severe Malaria
url: https://github.com/Stije/SevereMalariaAnalysis
- type: Article
diff --git a/src/codecs/jats/__file_snapshots__/elife-46472-v3.jats.xml b/src/codecs/jats/__file_snapshots__/elife-46472-v3.jats.xml
index 8b32fd7cd..87f2a045b 100644
--- a/src/codecs/jats/__file_snapshots__/elife-46472-v3.jats.xml
+++ b/src/codecs/jats/__file_snapshots__/elife-46472-v3.jats.xml
@@ -4449,6 +4449,7 @@
2012
+
]
diff --git a/src/codecs/jats/__file_snapshots__/elife-46472-v3.yaml b/src/codecs/jats/__file_snapshots__/elife-46472-v3.yaml
index 8f01ccc5e..960b1b5f3 100644
--- a/src/codecs/jats/__file_snapshots__/elife-46472-v3.yaml
+++ b/src/codecs/jats/__file_snapshots__/elife-46472-v3.yaml
@@ -4559,6 +4559,9 @@ references:
datePublished:
type: Date
value: '2012'
+ isPartOf:
+ type: Periodical
+ name: December 12, 2012; Published at US008697359B1 (Awarded)
title: Systems methods and compositions for sequence manipulation
url: https://patents.google.com/patent/WO2015089486A3/en
title:
diff --git a/src/codecs/jats/__file_snapshots__/elife-46793-v1.jats.xml b/src/codecs/jats/__file_snapshots__/elife-46793-v1.jats.xml
index a80b15dd9..99062c871 100644
--- a/src/codecs/jats/__file_snapshots__/elife-46793-v1.jats.xml
+++ b/src/codecs/jats/__file_snapshots__/elife-46793-v1.jats.xml
@@ -3942,6 +3942,7 @@
[
+ FASTQ/A Short-Reads Pre-Processing Tools
Gordon
@@ -5121,6 +5122,7 @@
2019
+
]
[
diff --git a/src/codecs/jats/__file_snapshots__/elife-46793-v1.yaml b/src/codecs/jats/__file_snapshots__/elife-46793-v1.yaml
index 4deab87df..267ec67b2 100644
--- a/src/codecs/jats/__file_snapshots__/elife-46793-v1.yaml
+++ b/src/codecs/jats/__file_snapshots__/elife-46793-v1.yaml
@@ -3236,6 +3236,7 @@ references:
datePublished:
type: Date
value: '2010'
+ title: "\_FASTQ/A Short-Reads Pre-Processing Tools"
url: http://hannonlab.cshl.edu/fastx_toolkit/download.html
- type: Article
id: bib50
@@ -4987,6 +4988,9 @@ references:
datePublished:
type: Date
value: '2019'
+ isPartOf:
+ type: Periodical
+ name: GitHub
title: GWscreen_G4sensitivity
url: https://github.com/sblab-bioinformatics/GWscreen_G4sensitivity
- type: Article
diff --git a/src/codecs/jats/__file_snapshots__/elife-52882-v2.jats.xml b/src/codecs/jats/__file_snapshots__/elife-52882-v2.jats.xml
index 3699c858d..652170ac7 100644
--- a/src/codecs/jats/__file_snapshots__/elife-52882-v2.jats.xml
+++ b/src/codecs/jats/__file_snapshots__/elife-52882-v2.jats.xml
@@ -11748,6 +11748,7 @@
2019
+
]
[
@@ -11760,6 +11761,7 @@
2019
+
]
[
diff --git a/src/codecs/jats/__file_snapshots__/elife-52882-v2.yaml b/src/codecs/jats/__file_snapshots__/elife-52882-v2.yaml
index 879d883c8..6cccd6274 100644
--- a/src/codecs/jats/__file_snapshots__/elife-52882-v2.yaml
+++ b/src/codecs/jats/__file_snapshots__/elife-52882-v2.yaml
@@ -1482,6 +1482,9 @@ references:
datePublished:
type: Date
value: '2019'
+ isPartOf:
+ type: Periodical
+ name: GitLab
title: Programs closed-loop phototaxis
url: https://gitlab.com/Phiasso/programs_closed-loop_phototaxis.git
- type: Article
@@ -1495,6 +1498,9 @@ references:
datePublished:
type: Date
value: '2019'
+ isPartOf:
+ type: Periodical
+ name: GitLab
title: Analysis behavioral phototaxis
url: https://gitlab.com/Phiasso/analysis.git
- type: Article
diff --git a/src/codecs/jats/index.ts b/src/codecs/jats/index.ts
index 7cb594b55..f5110b578 100644
--- a/src/codecs/jats/index.ts
+++ b/src/codecs/jats/index.ts
@@ -1351,35 +1351,46 @@ export function decodeReference(
let title: string | undefined
let isPartOf: stencila.CreativeWork | undefined
- if (publicationType === 'journal' || publicationType === 'preprint') {
+ let chapterTitle: string | undefined
+
+ // Assign the title based upon the publicationType
+ if (['journal', 'preprint'].includes(publicationType ?? '')) {
title = textOrUndefined(child(elem, 'article-title'))
+ } else if (['book', 'report'].includes(publicationType ?? '')) {
+ chapterTitle = textOrUndefined(child(elem, 'chapter-title'))
+ // Not a chapter so title is ]