Commit adf43eb7 authored by lindenb's avatar lindenb
Browse files

cont

parent a615ef15
......@@ -93,44 +93,38 @@ curl "https://en.wikipedia.org/wiki/Main_Page"
\subsection{xmllint}
Exemple 1:
Exemple 1: formatter wikipedia
\begin{lstlisting}[language=bash]
curl "https://en.wikipedia.org/wiki/Main_Page" | xmllint --format -
\end{lstlisting}
Exemple 2:
Exemple 2: affiche les 'href' dans wikipedia
\begin{lstlisting}[language=bash]
curl "https://en.wikipedia.org/wiki/Main_Page" | xmllint --xpath '//a/@href' -
\end{lstlisting}
Exemple 3:
Exemple 3: compte les 'href' dans wikipedia
\begin{lstlisting}[language=bash]
curl -s "https://en.wikipedia.org/wiki/Main_Page" | xmllint --xpath 'count(//a/@href)' -
\end{lstlisting}
\section{NCBI-EUtils}
%%\begin{frame}[fragile]
\subsection{XML}
\subsection{XSLT}
\remoteimage{jeter02.png}{https://upload.wikimedia.org/wikipedia/commons/thumb/6/68/XML.svg/500px-XML.svg.png}{scale=0.3}
%%\end{frame}
%%\begin{frame}[fragile]
\subsection{XSLT}
\remoteimage{jeter03.png}{https://upload.wikimedia.org/wikipedia/commons/thumb/e/e6/XSLT_en.svg/231px-XSLT_en.svg.png}{scale=0.4}
%%\end{frame}
%%\begin{frame}[fragile]
\subsection{XSLTPROC}
\begin{lstlisting}[language=bash]
xsltproc stylesheet.xsl file.xml > result.xml
\end{lstlisting}
%%\end{frame}
\section{NCBI-EUtils}
\subsection{Formats}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%
%% FORMAT
......@@ -139,9 +133,11 @@ xsltproc stylesheet.xsl file.xml > result.xml
%\hugeslide{Formats}
%%\begin{frame}[fragile]
\subsection{Formats}
\subsubsection{Genbank}
\url{http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=25&rettype=gb}
\begin{lstlisting}[basicstyle=\tiny,breaklines=false]
LOCUS X53813 422 bp DNA linear MAM 22-JUN-1992
DEFINITION Blue Whale heavy satellite DNA.
......@@ -185,7 +181,7 @@ ORIGIN
%%\begin{frame}[fragile]
\url{http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=25}
\subsection{Formats}
\subsubsection{ASN.1}
\begin{lstlisting}[basicstyle=\tiny,breaklines=false]
Seq-entry ::= seq {
......@@ -223,7 +219,7 @@ Seq-entry ::= seq {
%%\begin{frame}[fragile]
\subsection{Formats}
\subsubsection{ASN.1 (schema)}
\url{http://www.ncbi.nlm.nih.gov/data_specs/asn/insdseq.asn}
\begin{lstlisting}[basicstyle=\tiny,breaklines=false]
......@@ -267,7 +263,7 @@ INSDSeq ::= SEQUENCE {
%%\end{frame}
%%\begin{frame}[fragile]
\subsection{Formats}
\subsubsection{ASN.1 (tools)}
\begin{center}
{\bf DATATOOL}\\
......@@ -317,7 +313,7 @@ actyla; Cetacea; Mysticeti; Balaenopteridae; Balaenoptera</GBSeq_taxonomy>
%%\begin{frame}[fragile]
\subsection{Formats}
\subsubsection{XML (DTD)}
\url{http://www.ncbi.nlm.nih.gov/dtd/NCBI_GBSeq.mod.dtd}
\begin{lstlisting}[language=xml,basicstyle=\tiny,breaklines=false]
......@@ -353,26 +349,22 @@ actyla; Cetacea; Mysticeti; Balaenopteridae; Balaenoptera</GBSeq_taxonomy>
%%\end{frame}
%\hugeslide{E-Utilities}
\section{E-Utilities}
%\hugeslide{GI}
%%\begin{frame}
\subsection{E-Utilities}
\begin{center}
Set of seven server-side programs that provide a stable interface to the search, retrieval, and linking functions of the Entrez system, using a fixed URL syntax.\\
The output provided by the E-Utilities is in XML format\\
\end{center}
%%\end{frame}
%%\begin{frame}
\subsection{GI}
unique identfier for object in the NCBI database (pubmed id, sequence gi...)
\subsection{Entrez Direct}
\begin{center}
\url{http://www.ncbi.nlm.nih.gov/books/NBK179288/}
"Entrez Direct (EDirect) is an advanced method for accessing the NCBI's set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window. Functions take search terms from command-line arguments. Individual operations are combined to build multi-step queries. Record retrieval and formatting normally complete the process."
\end{center}
%%\end{frame}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
......@@ -385,10 +377,10 @@ The output provided by the E-Utilities is in XML format\\
%%\begin{frame}[fragile]
\subsection{EInfo}
\begin{center}
Provides a {\bf list of the names of all valid Entrez databases}.\\
Provides statistics for a single database, including lists of indexing fields and available link names.
\end{center}
%%\end{frame}
%%\begin{frame}[fragile]
......@@ -435,7 +427,6 @@ Base URL:
%%\begin{frame}[fragile]
\subsection{EInfo}
Return statistics for a given Entrez database:\\
\small
\url{http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=DbName}
......@@ -443,7 +434,7 @@ Return statistics for a given Entrez database:\\
%%\begin{frame}[fragile]
\subsection{EInfo}
\subsubsection{Statistics for Pubmed}
\url{http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=pubmed}
\begin{lstlisting}[language=xml,basicstyle=\tiny,breaklines=false]
......@@ -476,7 +467,7 @@ Return statistics for a given Entrez database:\\
%%\end{frame}
%%\begin{frame}[fragile]
\subsection{EInfo}
\subsubsection{Statistics for Pubmed}
\url{http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=pubmed}
\begin{lstlisting}[language=xml,basicstyle=\tiny,breaklines=false]
......@@ -515,18 +506,17 @@ issions as well as automated searching of PubMed abstracts and full-text PubMed
%% GQuery
%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%\hugeslide{GQuery}
%%\begin{frame}[fragile]
\subsection{GQuery}
Provides the number of records retrieved in all Entrez databases by a single text query.
%%\end{frame}
%%\begin{frame}[fragile]
\subsection{GQuery}
\subsubsection{Example}
\begin{lstlisting}[language=bash,basicstyle=\tiny,breaklines=true,escapechar=\!]
$ curl "http://eutils.ncbi.nlm.nih.gov/gquery?term=tyrannosaurus%20rex&retmode=xml"
......@@ -551,7 +541,7 @@ $ curl "http://eutils.ncbi.nlm.nih.gov/gquery?term=tyrannosaurus%20rex&retmode=
%%\begin{frame}[fragile]
\subsection{GQuery}
\subsubsection{Transforming to HTML using XSLT}
The XSLT stylesheet.
......@@ -588,13 +578,14 @@ The XSLT stylesheet.
%%\end{frame}
%%\begin{frame}[fragile]
\subsection{GQuery}
\subsubsection{Transforming to HTML}
\begin{lstlisting}[language=bash,basicstyle=\tiny,breaklines=true]
$ curl "http://eutils.ncbi.nlm.nih.gov/gquery?term=tyrannosaurus%20rex&retmode=xml" |\
xsltproc gquery2html.xsl -
\end{lstlisting}
\begin{lstlisting}[language=html,basicstyle=\tiny,breaklines=false]
<html>
<body>
......@@ -649,14 +640,12 @@ The XSLT stylesheet.
%%\begin{frame}[fragile]
\subsection{ESearch}
\subsubsection{Syntax}
Base URL
\url{http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi}
%%\end{frame}
%%\begin{frame}[fragile]
\subsection{ESearch}
\subsubsection{Searching for 'Mammuthus primigenius' }
\begin{lstlisting}[language=bash,basicstyle=\tiny,breaklines=true]
curl "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nucleotide&term=%22Mammuthus%20primigenius%22%5BORGN%5D" |\
......@@ -711,7 +700,6 @@ xmllint --format -
%%\end{frame}
%%\begin{frame}[fragile]
\subsection{ESearch}
\subsubsection{the retmax parameter }
\begin{lstlisting}[language=bash,basicstyle=\tiny,breaklines=true]
curl "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nucleotide&term=%22Mammuthus%20primigenius%22%5BORGN%5D&retmax=2" |\
......@@ -749,7 +737,6 @@ xmllint --format -
%%\begin{frame}[fragile]
\subsection{ESearch}
\subsubsection{the retstart parameter }
\begin{lstlisting}[language=bash,basicstyle=\tiny,breaklines=true]
curl "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nucleotide&term=%22Mammuthus%20primigenius%22%5BORGN%5D&retmax=3&retstart=100" |\
......@@ -787,7 +774,7 @@ xmllint --format -
%%\end{frame}
%%\begin{frame}[fragile]
\subsection{ESearch}
\subsubsection{rettype=retcount }
\begin{lstlisting}[language=bash,basicstyle=\tiny,breaklines=true]
curl "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nucleotide&term=%22Mammuthus%20primigenius%22%5BORGN%5D&rettype=count" |\
......@@ -807,9 +794,7 @@ xmllint --format -
%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%\hugeslide{ESummary}
%%\begin{frame}[fragile]
\subsection{ESummary}
\subsubsection{Syntax}
\begin{itemize}
......
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