diff --git a/.DS_Store b/.DS_Store index fb316e2..abc2116 100644 Binary files a/.DS_Store and b/.DS_Store differ diff --git a/.nojekyll b/.nojekyll index 92fc501..5b09896 100644 --- a/.nojekyll +++ b/.nojekyll @@ -1 +1 @@ -d399bd41 \ No newline at end of file +ceedc812 \ No newline at end of file diff --git a/References.html b/References.html index c07f586..4f83b8d 100644 --- a/References.html +++ b/References.html @@ -136,6 +136,21 @@ Home + @@ -199,9 +236,27 @@
+
+Crystal-Ornelas, Robert, Charuleka Varadharajan, Dylan O’Ryan, Kathleen Beilsmith, Benjamin Bond-Lamberty, Kristin Boye, Madison Burrus, et al. 2022. “Enabling FAIR Data in Earth and Environmental Science with Community-Centric (Meta)data Reporting Formats.” Sci Data 9 (1): 700. +
+
+Oldoni, Fabio, Kenneth K Kidd, and Daniele Podini. 2019. “Microhaplotypes in Forensic Genetics.” Forensic Sci. Int. Genet. 38 (January): 54–69. +
+
+SRA Metadata and Submission Overview.” n.d. https://www.ncbi.nlm.nih.gov/sra/docs/submitmeta/. +
Tessema, Sofonias K, Nicholas J Hathaway, Noam B Teyssier, Maxwell Murphy, Anna Chen, Ozkan Aydemir, Elias M Duarte, et al. 2022. “Sensitive, Highly Multiplexed Sequencing of Microhaplotypes from the Plasmodium Falciparum Heterozygome.” J. Infect. Dis. 225 (April): 1227–37.
+
+Vangay Pajau, Burgin Josephine, Johnston Anjanette, Beck Kristen L., Berrios Daniel C., Blumberg Kai, Canon Shane, et al. 2021. “Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative’s Workshop and Follow-On Activities.” mSystems 6 (1): e01194–20. +
+
+Weisenhorn, Pamela, and Kathleen Beilsmith. 2022. ESS-DIVE Reporting Format for Amplicon Abundance Table.” Environmental System Science Data Infrastructure for a Virtual Ecosystem; Environmental Systems Science Data Infrastructure for a Virtual Ecosystem (ESS-DIVE). +
+
+Yilmaz, Pelin, Renzo Kottmann, Dawn Field, Rob Knight, James R Cole, Linda Amaral-Zettler, Jack A Gilbert, et al. 2011. “Minimum Information about a Marker Gene Sequence (MIMARKS) and Minimum Information about Any (x) Sequence (MIxS) Specifications.” Nat. Biotechnol. 29 (5): 415–20. +
@@ -351,7 +406,7 @@ } var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//); var mailtoRegex = new RegExp(/^mailto:/); - var filterRegex = new RegExp("https:\/\/PlasmoGenEpi\.github\.io\/Portable_Microhaplotype_Object_Tools\/"); + var filterRegex = new RegExp("https:\/\/PlasmoGenEpi\.github\.io\/PMO_Docs\/"); var isInternal = (href) => { return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href); } diff --git a/Tools_Installation/pmotools-python_installation.html b/Tools_Installation/pmotools-python_installation.html index 4ee3cd1..8f61883 100644 --- a/Tools_Installation/pmotools-python_installation.html +++ b/Tools_Installation/pmotools-python_installation.html @@ -116,6 +116,21 @@ Home + @@ -413,7 +450,7 @@ } var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//); var mailtoRegex = new RegExp(/^mailto:/); - var filterRegex = new RegExp("https:\/\/PlasmoGenEpi\.github\.io\/Portable_Microhaplotype_Object_Tools\/"); + var filterRegex = new RegExp("https:\/\/PlasmoGenEpi\.github\.io\/PMO_Docs\/"); var isInternal = (href) => { return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href); } diff --git a/format/FormatExample.html b/format/FormatExample.html new file mode 100644 index 0000000..e116d8a --- /dev/null +++ b/format/FormatExample.html @@ -0,0 +1,802 @@ + + + + + + +PMO Examples – Portable Microhaplotype Object (PMO) + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + + + \ No newline at end of file diff --git a/format/FormatOverview.html b/format/FormatOverview.html new file mode 100644 index 0000000..fe85487 --- /dev/null +++ b/format/FormatOverview.html @@ -0,0 +1,3425 @@ + + + + + + +PMO fields overview – Portable Microhaplotype Object (PMO) + + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + + + \ No newline at end of file diff --git a/format/PathWeaverHeome1_PMO.json.gz b/format/PathWeaverHeome1_PMO.json.gz new file mode 100644 index 0000000..2c3ea10 Binary files /dev/null and b/format/PathWeaverHeome1_PMO.json.gz differ diff --git a/format/moz2018_PMO.json.gz b/format/moz2018_PMO.json.gz new file mode 100644 index 0000000..481afc1 Binary files /dev/null and b/format/moz2018_PMO.json.gz differ diff --git a/index.html b/index.html index 92bc2a4..81202a2 100644 --- a/index.html +++ b/index.html @@ -51,7 +51,27 @@ @media screen { pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; } } - +/* CSS for citations */ +div.csl-bib-body { } +div.csl-entry { + clear: both; + margin-bottom: 0em; +} +.hanging-indent div.csl-entry { + margin-left:2em; + text-indent:-2em; +} +div.csl-left-margin { + min-width:2em; + float:left; +} +div.csl-right-inline { + margin-left:2em; + padding-left:1em; +} +div.csl-indent { + margin-left: 2em; +} @@ -116,6 +136,21 @@ Home + @@ -159,17 +216,52 @@