first draft of the site

pgroth · Nov 4, 2018 · acfa9efd2a4a14d777cd07bd9cb4c702c4a77062 · acfa9ef
1 parent 2cd89e1
commit acfa9efd2a4a14d777cd07bd9cb4c702c4a77062
diff --git a/Gemfile b/Gemfile
@@ -0,0 +1,10 @@
+source 'https://rubygems.org'
+group :jekyll_plugins do
+    gem 'github-pages'
+    gem 'jekyll'
+    gem 'jekyll-email-protect'
+    gem 'jekyll-paginate'
+    gem 'jekyll-scholar'
+    gem 'jemoji'
+    gem 'unicode_utils'
+end
diff --git a/LICENSE b/LICENSE
@@ -0,0 +1,20 @@
+The MIT License (MIT)
+
+Copyright (c) 2018 Maruan Al-Shedivat.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the "Software"), to deal in
+the Software without restriction, including without limitation the rights to
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
+the Software, and to permit persons to whom the Software is furnished to do so,
+subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
diff --git a/README.md b/README.md
@@ -1 +1,4 @@
-## Welcome
+Website of the INelligent Data Integration Lab (INDE Lab) at the University of Amsterdam
+
+
+Powered by [Jekyll](http://jekyllrb.com/) using the [al-folio](https://github.com/alshedivat/al-folio)
diff --git a/_bibliography/papers.bib b/_bibliography/papers.bib
@@ -0,0 +1,181 @@
+---
+---
+@inproceedings{DBLP:conf/coling/GrothLSD18,
+  author    = {Paul T. Groth and
+               Michael Lauruhn and
+               Antony Scerri and
+               Ron Daniel},
+  title     = {Open Information Extraction on Scientific Text: An Evaluation},
+  booktitle = {Proceedings of the 27th International Conference on Computational
+               Linguistics, {COLING} 2018, Santa Fe, New Mexico, USA, August 20-26,
+               2018},
+  pages     = {3414--3423},
+  year      = {2018},
+  crossref  = {DBLP:conf/coling/2018},
+  url       = {https://aclanthology.info/papers/C18-1289/c18-1289},
+  timestamp = {Wed, 15 Aug 2018 11:10:27 +0200},
+  biburl    = {https://dblp.org/rec/bib/conf/coling/GrothLSD18},
+  bibsource = {dblp computer science bibliography, https://dblp.org}
+}
+
+@inproceedings{DBLP:conf/semweb/DeJongBDHMOSSST18,
+  author    = {Alex DeJong and
+               Radmila Bord and
+               Will Dowling and
+               Rinke Hoekstra and
+               Ryan Moquin and
+               Charlie O and
+               Mevan Samarasinghe and
+               Paul Snyder and
+               Craig Stanley and
+               Anna Tordai and
+               Michael Trefry and
+               Paul T. Groth},
+  title     = {Elsevier's Healthcare Knowledge Graph and the Case for Enterprise
+               Level Linked Data Standards},
+  booktitle = {Proceedings of the {ISWC} 2018 Posters {\&} Demonstrations, Industry
+               and Blue Sky Ideas Tracks co-located with 17th International Semantic
+               Web Conference {(ISWC} 2018), Monterey, USA, October 8th - to - 12th,
+               2018.},
+  year      = {2018},
+  crossref  = {DBLP:conf/semweb/2018p},
+  url       = {http://ceur-ws.org/Vol-2180/paper-85.pdf},
+  timestamp = {Thu, 11 Oct 2018 12:45:11 +0200},
+  biburl    = {https://dblp.org/rec/bib/conf/semweb/DeJongBDHMOSSST18},
+  bibsource = {dblp computer science bibliography, https://dblp.org}
+}
+
+@inproceedings{DBLP:conf/semweb/LauruhnGHD18,
+  author    = {Michael Lauruhn and
+               Paul T. Groth and
+               Corey A. Harper and
+               Helena F. Deus},
+  title     = {Use of Internal Testing Data to Help Determine Compensation for Crowdsourcing
+               Tasks},
+  booktitle = {Proceedings of the 2nd International Workshop on Augmenting Intelligence
+               with Humans{\-}-in-{\-}the-{\-}Loop co-located with 17th International
+               Semantic Web Conference {(ISWC} 2018), Monterey, California, October
+               9th, 2018.},
+  pages     = {27--37},
+  year      = {2018},
+  crossref  = {DBLP:conf/semweb/2018huml},
+  url       = {http://ceur-ws.org/Vol-2169/paper-04.pdf},
+  timestamp = {Mon, 29 Oct 2018 16:50:54 +0100},
+  biburl    = {https://dblp.org/rec/bib/conf/semweb/LauruhnGHD18},
+  bibsource = {dblp computer science bibliography, https://dblp.org}
+}
+
+@article{DBLP:journals/tkde/WylotCHG17,
+  author    = {Marcin Wylot and
+               Philippe Cudr{\'{e}}{-}Mauroux and
+               Manfred Hauswirth and
+               Paul T. Groth},
+  title     = {Storing, Tracking, and Querying Provenance in Linked Data},
+  journal   = {{IEEE} Trans. Knowl. Data Eng.},
+  volume    = {29},
+  number    = {8},
+  pages     = {1751--1764},
+  year      = {2017},
+  url       = {https://doi.org/10.1109/TKDE.2017.2690299},
+  doi       = {10.1109/TKDE.2017.2690299},
+  timestamp = {Tue, 18 Jul 2017 10:49:06 +0200},
+  biburl    = {https://dblp.org/rec/bib/journals/tkde/WylotCHG17},
+  bibsource = {dblp computer science bibliography, https://dblp.org}
+}
+
+@article{DBLP:journals/toit/Stamatogiannakis17,
+  author    = {Manolis Stamatogiannakis and
+               Elias Athanasopoulos and
+               Herbert Bos and
+               Paul T. Groth},
+  title     = {{PROV2R: Practical Provenance Analysis of Unstructured
+               Processes}},
+  journal   = {{ACM} Trans. Internet Techn.},
+  volume    = {17},
+  number    = {4},
+  pages     = {37:1--37:24},
+  year      = {2017},
+  url       = {https://doi.org/10.1145/3062176},
+  doi       = {10.1145/3062176},
+  timestamp = {Fri, 02 Nov 2018 09:33:33 +0100},
+  biburl    = {https://dblp.org/rec/bib/journals/toit/Stamatogiannakis17},
+  bibsource = {dblp computer science bibliography, https://dblp.org}
+}
+
+@article{10.7717/peerj.3997,
+ title = {Indicators for the use of robotic labs in basic biomedical research: a literature analysis},
+ author = {Groth, Paul and Cox, Jessica},
+ year = 2017,
+ month = nov,
+ keywords = {Robotic labs, Indicators, Text mining, Methods, Literature analysis},
+ abstract = {
+            Robotic labs, in which experiments are carried out entirely by robots, have the potential to provide a reproducible and transparent foundation for performing basic biomedical laboratory experiments. In this article, we investigate whether these labs could be applicable in current experimental practice. We do this by text mining 1,628 papers for occurrences of methods that are supported by commercial robotic labs. Using two different concept recognition tools, we find that 86%–89% of the papers have at least one of these methods. This and our other results provide indications that robotic labs can serve as the foundation for performing many lab-based experiments.
+         },
+ volume = 5,
+ pages = {e3997},
+ journal = {PeerJ},
+ issn = {2167-8359},
+ url = {https://doi.org/10.7717/peerj.3997},
+ doi = {10.7717/peerj.3997}
+}
+
+@incollection{DBLP:books/sp/17/HauswirthWGGC17,
+  author    = {Manfred Hauswirth and
+               Marcin Wylot and
+               Martin Grund and
+               Paul T. Groth and
+               Philippe Cudr{\'{e}}{-}Mauroux},
+  title     = {Linked Data Management},
+  booktitle = {Handbook of Big Data Technologies},
+  pages     = {307--338},
+  year      = {2017},
+  crossref  = {DBLP:books/sp/ZS2017},
+  url       = {https://doi.org/10.1007/978-3-319-49340-4\_9},
+  doi       = {10.1007/978-3-319-49340-4\_9},
+  timestamp = {Fri, 02 Nov 2018 09:27:05 +0100},
+  biburl    = {https://dblp.org/rec/bib/books/sp/17/HauswirthWGGC17},
+  bibsource = {dblp computer science bibliography, https://dblp.org}
+}
+
+@inproceedings{DBLP:conf/akbc/GrothPMAD16,
+  author    = {Paul T. Groth and
+               Sujit Pal and
+               Darin McBeath and
+               Brad Allen and
+               Ron Daniel},
+  title     = {Applying Universal Schemas for Domain Specific Ontology Expansion},
+  booktitle = {Proceedings of the 5th Workshop on Automated Knowledge Base Construction,
+               AKBC@NAACL-HLT 2016, San Diego, CA, USA, June 17, 2016},
+  pages     = {81--85},
+  year      = {2016},
+  crossref  = {DBLP:conf/akbc/2016},
+  url       = {http://aclweb.org/anthology/W/W16/W16-1315.pdf},
+  timestamp = {Wed, 05 Oct 2016 13:56:02 +0200},
+  biburl    = {https://dblp.org/rec/bib/conf/akbc/GrothPMAD16},
+  bibsource = {dblp computer science bibliography, https://dblp.org}
+}
+
+@article{fairprinciples2016,
+title = "The FAIR Guiding Principles for scientific data management and stewardship",
+abstract = "There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders-representing academia, industry, funding agencies, and scholarly publishers-have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.",
+author = "Wilkinson, {Mark D.} and Michel Dumontier and Aalbersberg, {IJsbrand Jan} and Gabrielle Appleton and Myles Axton and Arie Baak and Niklas Blomberg and Boiten, {Jan Willem} and {da Silva Santos}, {Luiz Bonino} and Bourne, {Philip E.} and Jildau Bouwman and Brookes, {Anthony J.} and Tim Clark and Merc{\`e} Crosas and Ingrid Dillo and Olivier Dumon and Scott Edmunds and Evelo, {Chris T.} and Richard Finkers and Alejandra Gonzalez-Beltran and Gray, {Alasdair J.G.} and Paul Groth and Carole Goble and Grethe, {Jeffrey S.} and Jaap Heringa and {'t Hoen}, {Peter A C} and Rob Hooft and Tobias Kuhn and Ruben Kok and Joost Kok and Lusher, {Scott J.} and Martone, {Maryann E} and Albert Mons and Packer, {Abel L.} and Bengt Persson and Philippe Rocca-Serra and Marco Roos and {van Schaik}, Rene and Sansone, {Susanna Assunta} and Erik Schultes and Thierry Sengstag and Ted Slater and George Strawn and Swertz, {Morris A.} and Mark Thompson and {Van Der Lei}, Johan and {Van Mulligen}, Erik and Jan Velterop and Andra Waagmeester and Peter Wittenburg and Katherine Wolstencroft and Jun Zhao and Barend Mons",
+year = "2016",
+doi = "10.1038/sdata.2016.18",
+language = "English",
+volume = "3",
+journal = "Scientific Data",
+issn = "2052-4463",
+publisher = "Nature Publishing Group",
+}
+
+@article{article,
+author = {Lauruhn, Michael and Groth, Paul},
+year = {2016},
+month = {11},
+pages = {},
+title = {Sources of Change for Modern Knowledge Organization Systems},
+volume = {43},
+journal = {KNOWLEDGE ORGANIZATION},
+doi = {10.5771/0943-7444-2016-8-622},
+arxiv = {1611.00217}
+}
diff --git a/_config.yml b/_config.yml
@@ -1 +1,85 @@
-remote_theme: broccolini/swiss
+# -----------------------------------------------------------------------------
+# Site settings
+# -----------------------------------------------------------------------------
+name: INDE Lab
+description: The Intelligent Data Engineering Lab (INDE Lab) at the University of Amsterdam
+
+footer_text:
+
+url: # the base hostname & protocol for your site
+baseurl: # the subpath of your site, e.g. /blog/
+last_updated: # leave blank if you don't want to display last updated
+
+# -----------------------------------------------------------------------------
+# Social integration
+# -----------------------------------------------------------------------------
+github_username: # your GitHub user name
+twitter_username: pgroth
+linkedin_username: # your LinkedIn user name
+scholar_userid: # your Google Scholar ID
+orcid_id: # your ORCID ID
+contact_note: #nothing
+
+#google_analytics: UA-XXXXXXXXX # out your google-analytics code
+
+future: true
+
+# -----------------------------------------------------------------------------
+# Collections
+# -----------------------------------------------------------------------------
+collections:
+  news:
+    defaults:
+      layout: post
+    output: true
+    permalink: /news/:path/
+
+news_limit: 5
+
+# -----------------------------------------------------------------------------
+# Jekyll settings
+# -----------------------------------------------------------------------------
+
+# Build settings
+markdown: kramdown
+highlighter: pygments
+
+# Includes & excludes
+include: ['_pages']
+exclude: ['vendor','future']
+
+# Plug-ins
+plugins:
+    - jekyll-email-protect
+    - jekyll-paginate
+    - jekyll/scholar
+    - jemoji
+
+# Jekyll-Scholar
+scholar:
+  last_name: groth
+  style: apa
+  locale: en
+
+  sort_by: year
+  order: descending
+
+  source: /_bibliography/
+  bibliography: papers.bib
+  bibliography_template: bib
+
+  replace_strings: true
+  join_strings: true
+
+  details_dir: bibliography
+  details_layout: bibtex.html
+  details_link: Details
+
+  query: "@*"
+
+# -----------------------------------------------------------------------------
+# Other settings
+# -----------------------------------------------------------------------------
+jquery_version: "1.12.4"
+katex_version: "0.9.0"
+anchorjs_version: "3.2.2"
diff --git a/_data/coauthors.yml b/_data/coauthors.yml
@@ -0,0 +1,2 @@
+Groth:
+    url: http://pgroth.com
diff --git a/_includes/footer.html b/_includes/footer.html
@@ -0,0 +1,11 @@
+<footer>
+
+  <div class="wrapper">
+    &copy; Copyright {{ site.time | date: '%Y' }} {{ site.name }}.
+    {{ site.footer_text }}
+    {% if site.last_updated %}
+        Last updated: {{ site.last_updated }}.
+    {% endif %}
+  </div>
+
+</footer>
diff --git a/_includes/head.html b/_includes/head.html
@@ -0,0 +1,13 @@
+<head>
+  <meta charset="utf-8">
+  <meta name="viewport" content="width=device-width initial-scale=1" />
+  <meta http-equiv="X-UA-Compatible" content="IE=edge">
+
+  <title>{{ site.name }}{% if page.title and page.url != "/" %} | {{ page.title }}{% endif %}</title>
+  <meta name="description" content="{{ site.description }}">
+
+  <link rel="shortcut icon" href="{{ '/assets/img/favicon.ico' | prepend: site.baseurl | prepend: site.url }}">
+
+  <link rel="stylesheet" href="{{ '/assets/css/main.css' | prepend: site.baseurl | prepend: site.url }}">
+  <link rel="canonical" href="{{ page.url | replace:'index.html','' | prepend: site.baseurl | prepend: site.url }}">
+</head>
diff --git a/_includes/header.html b/_includes/header.html
@@ -0,0 +1,46 @@
+<header class="site-header">
+
+  <div class="wrapper">
+
+    {% if page.layout != "about" %}
+    <span class="site-title">
+        {% assign name = site.name | split: ' ' %}
+        <strong>{{ name | first }}</strong> {{ name | last }}
+    </span>
+    {% endif %}
+
+    <nav class="site-nav">
+      <input type="checkbox" id="nav-trigger" class="nav-trigger" />
+        <label for="nav-trigger">
+          <span class="menu-icon">
+            <svg viewBox="0 0 18 15" width="18px" height="15px">
+              <path fill="#424242" d="M18,1.484c0,0.82-0.665,1.484-1.484,1.484H1.484C0.665,2.969,0,2.304,0,1.484l0,0C0,0.665,0.665,0,1.484,0 h15.031C17.335,0,18,0.665,18,1.484L18,1.484z"/>
+              <path fill="#424242" d="M18,7.516C18,8.335,17.335,9,16.516,9H1.484C0.665,9,0,8.335,0,7.516l0,0c0-0.82,0.665-1.484,1.484-1.484 h15.031C17.335,6.031,18,6.696,18,7.516L18,7.516z"/>
+              <path fill="#424242" d="M18,13.516C18,14.335,17.335,15,16.516,15H1.484C0.665,15,0,14.335,0,13.516l0,0 c0-0.82,0.665-1.484,1.484-1.484h15.031C17.335,12.031,18,12.696,18,13.516L18,13.516z"/>
+            </svg>
+          </span>
+        </label>
+
+      <div class="trigger">
+        <!-- About -->
+        <a class="page-link" href="{{ site.baseurl | prepend: site.url }}/">about</a>
+
+        <!-- Blog
+        <a class="page-link" href="{{ '/blog/' | prepend: site.baseurl | prepend: site.url }}">blog</a>  -->
+
+        <!-- Pages -->
+        {% for page in site.pages %}
+          {% if page.title and page.url != "/" %}
+            <a class="page-link" href="{{ page.url | prepend: site.baseurl | prepend: site.url }}">{{ page.title }}</a>
+          {% endif %}
+        {% endfor %}
+
+        <!-- CV link -->
+        <!-- <a class="page-link" href="{{ '/assets/pdf/CV.pdf' | prepend: site.baseurl | prepend: site.url }}">vitae</a> -->
+
+      </div>
+    </nav>
+
+  </div>
+
+</header>